Academic literature on the topic 'One locus segregating'
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Journal articles on the topic "One locus segregating"
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Echt, C. S., K. K. Kidwell, S. J. Knapp, T. C. Osborn, and T. J. McCoy. "Linkage mapping in diploid alfalfa (Medicago sativa)." Genome 37, no. 1 (February 1, 1994): 61–71. http://dx.doi.org/10.1139/g94-008.
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A genome map of cultivated alfalfa was constructed using segregating restriction fragment length polymorphisms (RFLPs) and random amplified polymorphic DNAs (RAPDs) in a diploid backcross population generated from noninbred parents. Among the 153 loci scored in 87 progeny, four segregation ratios were observed for codominant and dominant markers: 1:1, 1:2:1, 1:1:1:1, and 3:1. Deviations from expected Mendelian ratios (p < 0.05) were observed for 34% of the loci studied. A genome map was assembled from two separate linkage maps, each constructed from a subset of the segregation data. One linkage map was constructed from 46 RFLP and 40 RAPD markers segregating 1:1 from the F1 parent of the backcross and the other linkage map was constructed from 33 RFLP and 28 RAPD markers segregating 1:1 from the recurrent parent. Sixteen loci with alleles segregating 1:1 from both parents were used as locus bridges to align individual linkage groups between the two maps. The combined use of RFLPs and RAPDs was an effective method for developing an alfalfa genome map.Key words: genome mapping, RAPD, RFLP, locus bridges.
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Rubino, David B. "Inheritance of Esterase, Diaphorase, and Glucose-6-phosphate Isomerase in Lisianthus." HortScience 28, no. 6 (June 1993): 661–63. http://dx.doi.org/10.21273/hortsci.28.6.661.
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Segregating lisianthus [Eustoma grandiflorum (Griseb.) Shinn.] progeny were evaluated to determine the inheritance of esterase (EST), diaphorase (DIA), and glucose-6-phosphate isomerase (GPI) isozymes. Phenotypic data supported the hypotheses that EST is monomeric and controlled by one locus (Est1) with at least three alleles, DIA is tetrameric and controlled by one locus (Dia2) with at least two alleles, and GPI is controlled by one locus (Gpil) with at least two alleles. The structure of the GPI isozyme could not be inferred from banding patterns. Joint segregation analyses indicated that the three loci segregate independently. These three isozymes are the first simply inherited, unlinked biochemical markers identified in lisianthus. These marker loci will be useful for genetic studies, breeding, and germplasm characterization.
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Havey, Michael J. "Genetic Mapping of Chartreuse Bulb Color in Onion." Journal of the American Society for Horticultural Science 145, no. 2 (March 2020): 110–19. http://dx.doi.org/10.21273/jashs04861-20.
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The most common bulb colors of onion (Allium cepa) are red, yellow, and white; chartreuse is a relatively rare bulb color conditioned by the homozygous recessive genotype at the G locus. In this research, plants with chartreuse bulbs were crossed with inbreds with yellow bulbs to develop segregating families for genetic mapping of the G locus. For all of 17 F2 families, segregations for yellow vs. chartreuse bulbs fit the expected 3:1 ratio (P > 0.05). DNAs were isolated from one F2 family and genotyped for single nucleotide polymorphisms (SNPs) to produce a genetic map of the G locus and 380 SNPs, of which 119 SNPs have not been previously mapped. Segregations for yellow vs. chartreuse bulbs placed the G locus at the end of chromosome 7 at 6.7 cM from the nearest SNP (isotig28625_2789). This codominant SNP marker linked to the G locus should be useful for introgression of recessive chartreuse bulb color into diverse onion populations for commercial production of this uniquely colored onion.
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Monnahan, Patrick J., and John K. Kelly. "Naturally segregating loci exhibit epistasis for fitness." Biology Letters 11, no. 8 (August 2015): 20150498. http://dx.doi.org/10.1098/rsbl.2015.0498.
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The extent to which gene interaction or epistasis contributes to fitness variation within populations remains poorly understood, despite its importance to a myriad of evolutionary questions. Here, we report a multi-year field study estimating fitness of Mimulus guttatus genetic lines in which pairs of naturally segregating loci exist in an otherwise uniform background. An allele at QTL x5b—a locus originally mapped for its effect on flower size—positively affects survival if combined with one genotype at quantitative trait locus x10a (aa) but has negative effects when combined with the other genotypes (Aa and AA). The viability differences between genotypes parallel phenotypic differences for the time and node at which a plant flowers. Viability is negatively correlated with fecundity across genotypes, indicating antagonistic pleiotropy for fitness components. This trade-off reduces the genetic variance for total fitness relative to the individual fitness components and thus may serve to maintain variation. Additionally, we find that the effects of each locus and their interaction often vary with the environment.
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Groover, A., M. Devey, T. Fiddler, J. Lee, R. Megraw, T. Mitchel-Olds, B. Sherman, S. Vujcic, C. Williams, and D. Neale. "Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine." Genetics 138, no. 4 (December 1, 1994): 1293–300. http://dx.doi.org/10.1093/genetics/138.4.1293.
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Abstract We report the identification of quantitative trait loci (QTL) influencing wood specific gravity (WSG) in an outbred pedigree of loblolly pine (Pinus taeda L.). QTL mapping in an outcrossing species is complicated by the presence of multiple alleles (> 2) at QTL and marker loci. Multiple alleles at QTL allow the examination of interaction among alleles at QTL (deviation from additive gene action). Restriction fragment length polymorphism (RFLP) marker genotypes and wood specific gravity phenotypes were determined for 177 progeny. Two RFLP linkage maps were constructed, representing maternal and paternal parent gamete segregations as inferred from diploid progeny RFLP genotypes. RFLP loci segregating for multiple alleles were vital for aligning the two maps. Each RFLP locus was assayed for cosegregation with WSG QTL using analysis of variance (ANOVA). Five regions of the genome contained one or more RFLP loci showing differences in mean WSG at or below the P = 0.05 level for progeny as grouped by RFLP genotype. One region contained a marker locus (S6a) whose QTL-associated effects were highly significant (P > 0.0002). Marker S6a segregated for multiple alleles, a prerequisite for determining the number of alleles segregating at the linked QTL and analyzing the interactions among QTL alleles. The QTL associated with marker S6a appeared to be segregating for multiple alleles which interacted with each other and with environments. No evidence for digenic epistasis was found among the five QTL.
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Lawson, Darlene M., Minou Hemmat, and Norman F. Weeden. "The Use of Molecular Markers to Analyze the Inheritance of Morphological and Developmental Traits in Apple." Journal of the American Society for Horticultural Science 120, no. 3 (May 1995): 532–37. http://dx.doi.org/10.21273/jashs.120.3.532.
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Five morphological and developmental traits (branching habit, vegetative budbreak, reproductive budbreak, bloom time, and root suckering) were analyzed in a family obtained from the apple (Malus domestica Borkh) cross `Rome Beauty' × `White Angel'. The phenotypic variation in these traits was compared with a selected set of marker loci covering the known genome of each of the parents to locate genes with major effects on the traits. The contrasting branching habits of the two parents appeared to be controlled by at least two loci. One of these, Tb, governed the presence or absence of lateral branches, particularly on the lower half of shoots. The locus was heterozygous in `White Angel' and was mapped to a 5 CM interval on linkage group 6. At least one other locus conditioning spur-type branching appeared to be segregating, but the locus or loci could not be linked to segregating markers. The timing of initial vegetative growth was tightly associated with the chromosomal region in which the Tb gene is located and maybe a pleiotropic effect of this gene. Time of reproductive budbreak correlated with segregation at the isozyme marker, Prx-c, on linkage group 5. Variation in time of bloom and later stages in flower development appeared to be controlled by different genes not linked to Prx-c. The tendency to produce root suckers cosegregated with a marker on `White Angel' linkage group 1, suggesting control by a single locus, Rs. Data from a `Rome Beauty' x `Robusta 5' family provided additional information on the inheritance of these traits.
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Mehlenbacher, Shawn A., and Maxine M. Thompson. "Inheritance of Style Color in Hazelnut." HortScience 39, no. 3 (June 2004): 475–76. http://dx.doi.org/10.21273/hortsci.39.3.475.
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The style color of standard hazelnut (Corylus avellana L.) cultivars ranges from pink to dark purple. Styles with an unusual yellow color were first noted in seedlings of the progeny `Goodpasture' × `Compton', and the ratio was ≈3 red: 1 yellow. Controlled crosses were made to investigate the genetic control of style color. The same 3:1 ratio was observed in four additional crosses in which both parents had red styles. Two crosses of a red and a yellow parent gave ≈50% yellow styles, while a cross of two selections with yellow styles gave only seedlings with yellow styles. These segregation ratios indicate control by a single locus, with yellow style color recessive to red. Seedlings with yellow styles have green buds and catkins and a more upright growth habit than their siblings with red styles. Inspection of the pedigrees of these progenies shows that `Daviana', `Willamette', `Butler', `Compton', `Goodpasture', and `Lansing #1' are heterozygous. `Daviana' appears to be the original source of the allele for yellow styles, as it is a known or suspected parent or ancestor of the others. Ratios in a progeny segregating simultaneously for growth habit (normal vs. contorted) and style color indicated independence of the traits. However, in a progeny segregating simultaneously for leaf color (red vs. green) and style color, no redleaf seedlings had yellow styles. The S-alleles of eight genotypes with yellow styles were determined, and indicate a possible linkage between the yellow style locus and the S locus that controls pollen-stigma incompatibility. One explanation is that the yellow style trait is conferred by an allele (ays) at the anthocyanin (A) locus that controls leaf color. A second explanation is that there is a yellow style locus closely linked to the A locus. The A locus is known to be loosely linked to the S locus.
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Labonne, J. D. J., A. Vaisman, and J. S. Shore. "Construction of a first genetic map of distylous Turnera and a fine-scale map of the S-locus region." Genome 51, no. 7 (July 2008): 471–78. http://dx.doi.org/10.1139/g08-031.
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As a prelude to discovery of genes involved in floral dimorphism and incompatibility, a genetic map of distylous Turnera was constructed along with a fine-scale map of the S-locus region. The genetic map consists of 79 PCR-based molecular markers (48 AFLP, 18 RAPD, 9 ISSR, 4 RAMP), 5 isozyme loci, one additional gene, and the S-locus, spanning a total distance of 683.3 cM. The 86 markers are distributed in 5 linkage groups, corresponding to the haploid chromosome number. Molecular markers tightly linked or co-segregating with the S-locus in an initial mapping population of 94 individuals were used to assay an additional 642 progeny to construct a map of the S-locus region. The fine-scale map consists of 2 markers (IS864a and RP45E9) flanking the S-locus at distances of 0.41 and 0.54 cM, respectively, and 3 additional markers (OPK14c, RP45G18, and RP81E18) co-segregating with the S-locus in the total mapping population of 736 individuals. The genetic map constructed will serve as a framework for localization of genes outside the S-locus affecting distyly, while molecular markers of the fine-scale map will be used to initiate chromosome walking to find the genes residing at the S-locus.
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Perry, D. J., and P. Knowles. "Inheritance and linkage relationships of allozymes of eastern white cedar (Thuja occidentalis) in northwestern Ontario." Genome 32, no. 2 (April 1, 1989): 245–50. http://dx.doi.org/10.1139/g89-435.
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Allozyme variants of 12 enzyme systems were examined in seed tissues of eastern white cedar (Thuja occidentalis L.), using starch gel electrophoresis. Nine loci were polymorphic and deviation from a 1:1 segregation ratio was observed between two of three alleles at one locus (Mdh-1). Of the possible 36 locus-pair combinations, 23 could be tested for linkage. Significant linkage was detected for three pairs of loci (Aat-1/Mdh-1, Aat-1/Pgm, and Idh-2/Me). Trees jointly segregating for Aat-1 and Pgm fell into two classes, one with a low recombination frequency (9.1%) and the other with a higher recombination frequency (26.6%). An inversion polymorphism is a possible cause of this linkage heterogeneity observed among trees.Key words: allozymes, isozymes, inheritance, linkage, eastern white cedar, northern white cedar, Thuja occidentalis L., Cupressaceae.
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Gao, Feng, Arvind H. Hirani, Jun Liu, Zheng Liu, Guohua Fu, Chunren Wu, Peter B. E. McVetty, and Genyi Li. "Fine Mapping a Clubroot Resistance Locus in Chinese Cabbage." Journal of the American Society for Horticultural Science 139, no. 3 (May 2014): 247–52. http://dx.doi.org/10.21273/jashs.139.3.247.
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There are various clubroot pathogen (Plasmodiophora brassicae) resistance genes within Brassica species with european turnip (B. rapa ssp. rapifera) being identified as potentially the best source of resistance for the development of clubroot-resistant cultivars in chinese cabbage (B. rapa ssp. pekinensis). To use clubroot resistance genes effectively, it is necessary to map these genes so that molecular markers inside or closely linked to these resistance genes can be developed. Using molecular marker-assisted selection, the clubroot resistance genes can be effectively transferred from cultivar to cultivar and from species to species. In this report, one clubroot resistance locus was mapped on linkage group A3 using five segregating populations developed from five chinese cabbage cultivars, suggesting that all the five cultivars shared the same clubroot resistance locus. Furthermore, one of these five chinese cabbage cultivars was used to develop a large segregating population to fine-map this clubroot resistance locus to a 187-kilobp chromosomal region. Molecular markers that are closely linked to the mapped clubroot resistance locus have been developed that can be used for marker-assisted selection in chinese cabbage and canola/rapeseed (B. rapa and B. napus) breeding programs.
Book chapters on the topic "One locus segregating"
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Rijsdijk, Frühling, and Pak Sham. "Genetic epidemiology 1: behavioural genetics." In Practical Psychiatric Epidemiology, 317–34. Oxford University Press, 2003. http://dx.doi.org/10.1093/med/9780198515517.003.0017.
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Behavioural genetics is the study of the genetic basis of behavioural traits including both psychiatric disorders and ‘normal’ personality dimensions. Behavioural genetics derives its theoretical basis from population genetics. Soon after the laws of Mendelian inheritance were re-discovered in 1900, the implications of these laws on the genetic properties of populations were worked out. Such properties include segregation ratios, genotypic frequencies in random mating populations, the effect of population structure and systems of mating, the impact of selection, the partitioning of genetic variance, and the genetic correlation between relatives. Some appreciation of population genetics is necessary for a deep understanding of behavioural genetics. Because of the complexity of behavioural traits, genetic factors cannot be regarded in isolation, or as static. Instead, it is important to consider: (i) the relative contributions of genetic and environmental factors, (ii) the interplay between genetic and environmental factors, and (iii) the changing role of genetic factors in different stages of development from infancy to old age. The major study designs in behavioural genetics will be discussed in this chapter, namely family studies, twin studies, and adoption studies. Behavioural genetics, augmented by molecular genetics has the potential to identify specific genetic variants which influence behaviour. This will be considered in detail in Chapter 14. Mendelian inheritance Gregor Mendel first demonstrated the genetic basis of biological inheritance by studies of simple all-or-none traits in the garden pea. These traits were particularly revealing because they were completely determined by the genotype at a single chromosomal locus. Diseases caused by genetic mutation at a single locus are commonly called Mendelian or single-gene disorders. A dominant disorder is expressed when an individual has one or two copies of the mutant allele, whereas a recessive disorder is expressed only when both alleles at the locus are the mutant variant. Examples of Mendelian disorders of clinical significance in psychiatry are Huntington's disease and fragile X syndrome. Mendelian disorders tend to be relatively rare because they are usually subjected to severe negative selective pressure, due to their increased mortality. Most common disorders and continuous traits of interest in psychiatry have an aetiology involving multiple genetic and environmental factors. Categorical and dimensional traits Behavioural genetics is rooted in both psychiatry and psychology. Psychiatrists traditionally adopt a medical model where diseases are defined as categorical entities and diagnoses are either present or absent. Psychologists on the other hand prefer quantitative measures of cognitive ability, personality and other traits. The methodology of behavioural genetics research reflects this duality, although there is a trend to integrate the two approaches, especially for traits such as anxiety and depression where both diagnostic criteria and quantitative measures exist.
Conference papers on the topic "One locus segregating"
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Bernardi, F., G. Marchetti, F. Vannini, L. Felloni, F. Panicucci, and F. Conconi. "SPORADISM INVESTIGATION AND CARRIER DETECTION IN HAEMOPHILIA A BY RFLP ANALYSIS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644011.
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Restriction fragment lenght polymorphisms (RFLPs)analysis has been employed for carrier detection andfor sporadism study in Haemophilia A. Three RFLPs, one intragenic in FC8 (647/BcII) and two with close linkage to Haemophilia A at DXS52 (Stl4/Taql) and DXS15 (DX13/BgIII), were used.In 20 families 29 carrier status determinations havebeen performed.In order to investigate sporadicity and to estimate the sex ratio of mutation rates directely, 17 families with isolated cases of haemophilia A were studied.In eight out of the 17 families the RFLPsanalysis excluded the carrier status of the maternalgrandmothers.Since by hemostatic studies the eight mothers of the propositi were shown to be haemophilia carriers, the origin of the newly mutated genes was inferred from the RFLP patterns: six haemophilic genes derive from the normal maternal grandfathers and two from the maternal grandmothers.Possible recombinations between FVIII locus and the extragenic RFLPs loci have to be considered; however the intragenic Bell RFLP is informative in five out of the eight families and the DXl3 and Stl4 patterns are concordant.The data indicate a higher mutation rate in males than in females gametes as previously suggested, althought not unanimously, by segregation analysis and coagulation studies. The RFLP analysis in a large number of families with isolated cases of haemophilia isnecessary to define the precise ratio of sex mutation rate for this disease.Work supported by P.F. Ing. Gen. Basi Mol. Mai. Ered. Contratto CNR N 8400877.
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Verweij, C. L., R. Quadt, E. Briët, and H. Pannekoek. "TWO VON WILLEBRAND FACTOR (vWF) GENE POLYMORPHISMS SEGREGATE WITH VON WILLEBRAND'S DISEASE (vWD) TYPE IIA: ASSIGNMENT OF THE DEFECTIVE GENE LOCUS IN vWD TYPE IIA." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644646.
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Patients with autosomal, dominant von Willebrand's disease (vWD) type IIA display a decreasedristocetin cofactor activity and lack the large and intermediate size von Willebrand factor (vWF) multimers. As yet the cause for this abnormal vWF protein is not known. In this study we determined whether vWD type IIA is due to a mutation in the vWF gene or by a defect in another gene involved, in for example, vWF processing.Restriction fragment-length polymorphisms (RFLP's), using the enzymes BgIII and XbaI in conjunction with human vWF cDNA probes, have been described. Restriction endonuclease analysis of genomic vWF DNA revealed that these genetic marker are located within the vWF gene. The vWF gene was determined to comprise about 160 kb and harbors at least 20 exons. The RFLP's were applied to study the segregation of alleles associated withvWD type IIA in a comprehensive, affected family. It is demonstrated that both RFLP's are completely linked with the vWD type-IIA trait. From this finding, we conclude that the defect, causing the vWD type IIA, is most likely due to a mutation in the vWF gene and not to a mutation in another gene involved in, for example, post-translational processing of the vWF protein.
Reports on the topic "One locus segregating"
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Levin, Ilan, John Thomas, Moshe Lapidot, Desmond McGrath, and Denis Persley. Resistance to Tomato yellow leaf curl virus (TYLCV) in tomato: molecular mapping and introgression of resistance to Australian genotypes. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7613888.bard.
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Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomatoes. Although first identified in the Mediterranean region, it is now distributed world-wide. Sequence analysis of the virus by the Australian group has shown that the virus is now present in Australia. Despite the importance of the disease and extensive research on the virus, very little is known about the resistance genes (loci) that determine host resistance and susceptibility to the virus. A symptom-less resistant line, TY-172, was developed at the Volcani Center which has shown the highest resistance level among all tested varieties. Preliminary results show that TY-172 is a good candidate to confer resistance to both TYLCV and to Tomato leaf curl virus (ToLCV) in Queensland conditions. Furthermore, Segregation analysis has previously indicated that the resistance is determined by 2-3 genes. In this proposal we aimed to substantiate that TY-172 can contribute to resistance breeding against TYLCV in Queensland, to develop DNA markers to advance such resistance breeding in both Israel and Queensland, and to exploit these markers for resistant breeding in Australian and Israeli lines. To map quantitative trait loci (QTLs) controlling TYLCVresistance in TY172, appropriate segregating populations were analyzed using 69 polymorphic DNA markers spanning the entire tomato genome. Results show that TYLCV resistance in TY172 is controlled by a previously unknown major QTL, originating from the resistant line, and four additional minor QTLs. The major QTL, termed Ty-5, maps to chromosome 4 and accounts for 39.7-to-46.6% of the variation in symptom severity among segregating plants (LOD score: 33-to-35). The minor QTLs, originated either from the resistant or susceptible parents, were mapped to chromosomes 1, 7, 9 and 11, and contributed 12% to the variation in symptom severity in addition to Ty-5. Further analysis of parental lines as well as large F₁, BC₁F₁, F₂ and BC₁F₂ populations originating from crosses carried out, in reciprocal manner, between TY172 and the susceptible processing line M-82 (LA3475) during spring-summer 2010, indicated that: (1) the minor QTLs we have previously identified are in effect not reproducible, (2)Ty-5 alone can yield highly resistant plants with practically no extra-chromosomal effects, and (3) the narrow-sense heritability estimate of resistance levels, attributed to additive factors responsive to selection, does not significantly deviate from 1. All of these results point to Ty-5 as the sole resistance locus in TY172 thus significantly increasing the likelihood of its successful molecular dissection. The DNA markers developed during the course of this study were transferred together with the TY172 genotype to Queensland. TY172 was crossed to a panel of Australian genotypes and the resulting populations were subjected to segregation analysis. Results showed that resistant locus, Ty-5, is highly reproducible in the Australian conditions as well. The Australian group was also able to make improvements to the marker assays by re-designing primer pairs to provide more robust PCR fragments. The Ty-5 locus has now been introgressed into elite Australian germplasm and selection for TYLCV resistance has begun. Cumulatively, our results show that Ty-5 can be effectively used, together with the TY172 genotype to expedite TYLCV resistance breeding and improve our understanding of the genetics that underline the response of tomato to TYLCV. Contributions to agriculture include: (1) the development of tools for more efficient resistance breeding, allowing the incorporation of resistance to local tomato varieties in Australia, Israel and elsewhere; and (2) establish a solid framework for a future attempt to clone the genes that encode such resistance. The latter will enable to decipher the resistance mechanisms that could be applied to other geminiviruses in tomato and possibly in other plant species.
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Ginzberg, Idit, and Walter De Jong. Molecular genetic and anatomical characterization of potato tuber skin appearance. United States Department of Agriculture, September 2008. http://dx.doi.org/10.32747/2008.7587733.bard.
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Potato (Solanum tuberosum L.) skin is composed of suberized phellem cells, the outer component of the tuber periderm. The focus of the proposed research was to apply genomic approaches to identify genes that control tuber skin appearance - smooth and shiny skin is highly preferred by the customers while russeted/netted skin potatoes are rejected. The breeding program (at Cornell University) seeks to develop smooth-skin varieties but has encountered frequent difficulties as inheritance of russeting involves complementary action by independently segregating genes, where a dominant allele at each locus is required for any degree of skin russeting. On the other hand, smooth-skin varieties frequently develop unsightly russeting in response to stress conditions, mainly high soil temperatures. Breeding programs in Israel aimed towards the improvement of heat tolerant varieties include skin quality as one of the desired characteristics. At the initiation of the present project it was unclear whether heat induced russeting and genetically inherited russeting share the same genes and biosynthesis pathways. Nevertheless, it has been suggested that russeting might result from increased periderm thickness, from strong cohesion between peridermal cells that prevents the outer layers from sloughing off, or from altered suberization processes in the skin. Hence, the original objectives were to conduct anatomical study of russet skin development, to isolate skin and russeting specific genes, to map the loci that determine the russet trait, and to compare with map locations the candidate russet specific genes, as well as to identify marker alleles that associated with russet loci. Anatomical studies suggested that russet may evolve from cracking at the outer layers of the skin, probably when skin development doesn’t meet the tuber expansion rate. Twodimensional gel electrophoresis and transcript profiling (cDNA chip, potato functional genomic project) indicated that in comparison to the parenchyma tissue, the skin is enriched with proteins/genes that are involved in the plant's responses to biotic and abiotic stresses and further expand the concept of the skin as a protective tissue containing an array of plantdefense components. The proteomes of skin from heat stressed tubers and native skin didn’t differ significantly, while transcript profiling indicated heat-related increase in three major functional groups: transcription factors, stress response and protein degradation. Exceptional was ACC synthase isogene with 4.6 fold increased level in the heat stressed skin. Russeting was mapped to two loci: rusB on chromosome 4 and rusC on chromosome 11; both required for russeting. No evidence was found for a third locus rusA that was previously proposed to be required for russeting. In an effort to find a link between the russeting character and the heat-induced russeting an attempt was made to map five genes that were found in the microarray experiment to be highly induced in the skin under heat stress in the segregating russet population. Only one gene was polymorphic; however it was localized to chromosome 2, so cannot correspond to rusB or rusC. Evaluation of AFLP markers tightly linked to rusB and rusC showed that these specific alleles are not associated with russeting in unrelated germplasm, and thus are not useful for MAS per se. To develop markers useful in applied breeding, it will be necessary to screen alleles of additional tightly linked loci, as well as to identify additional russet (heat-induced and/or native) related genes.
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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.
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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
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Fahima, Tzion, and Jorge Dubcovsky. Map-based cloning of the novel stripe rust resistance gene YrG303 and its use to engineer 1B chromosome with multiple beneficial traits. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598147.bard.
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Research problem: Bread wheat (Triticumaestivum) provides approximately 20% of the calories and proteins consumed by humankind. As the world population continues to increase, it is necessary to improve wheat yields, increase grain quality, and minimize the losses produced by biotic and abiotic stresses. Stripe rust, caused by Pucciniastriiformisf. sp. tritici(Pst), is one of the most destructive diseases of wheat. The new pathogen races are more virulent and aggressive than previous ones and have produced large economic losses. A rich source for stripe-rust resistance genes (Yr) was found in wild emmer wheat populations from Israel. Original Project goals: Our long term goal is to identify, map, clone, characterize and deploy in breeding, novel wild emmer Yr genes, and combine them with multiple beneficial traits. The current study was aiming to map and clone YrG303 and Yr15, located on chromosome 1BS and combine them with drought resistance and grain quality genes. Positional cloning of YrG303/Yr15: Fine mapping of these genes revealed that YrG303 is actually allelic to Yr15. Fine genetic mapping using large segregating populations resulted in reduction of the genetic interval spanning Yr15 to less than 0.1 cM. Physical mapping of the YrG303/Yr15 locus was based on the complete chromosome 1BS physical map of wheat constructed by our group. Screening of 1BS BAC library with Yr15 markers revealed a long BAC scaffold covering the target region. The screening of T. dicoccoidesaccession-specific BAC library with Yr15 markers resulted in direct landing on the target site. Sequencing of T. dicoccoidesBAC clones that cover the YrG303/Yr15 locus revealed a single candidate gene (CG) with conserved domains that may indicate a role in disease resistance response. Validation of the CG was carried out using EMS mutagenesis (loss-of- function approach). Sequencing of the CG in susceptible yr15/yrG303 plants revealed three independent mutants that harbour non-functional yr15/yrG303 alleles within the CG conserved domains, and therefore validated its function as a Pstresistance gene. Evaluation of marker-assisted-selection (MAS) for Yr15. Introgressions of Yr15 into cultivated wheat are widely used now. Recently, we have shown that DNA markers linked to Yr15 can be used as efficient tools for introgression of Yr15 into cultivated wheat via MAS. The developed markers were consistent and polymorphic in all 34 tested introgressions and are the most recommended markers for the introgression of Yr15. These markers will facilitate simultaneous selection for multiple Yr genes and help to avoid escapees during the selection process. Engineering of improved chromosome 1BS that harbors multiple beneficial traits. We have implemented the knowledge and genetic resources accumulated in this project for the engineering of 1B "super-chromosome" that harbors multiple beneficial traits. We completed the generation of a chromosome including the rye 1RS distal segment associated with improved drought tolerance with the Yr gene, Yr15, and the strong gluten allele 7Bx-over-expressor (7Bxᴼᴱ). We have completed the introgression of this improved chromosome into our recently released variety Patwin-515HP and our rain fed variety Kern, as well as to our top breeding lines UC1767 and UC1745. Elucidating the mechanism of resistance exhibited by Yr36 (WKS1). The WHEAT KINASE START1 (WKS1) resistance gene (Yr36) confers partial resistance to Pst. We have shown that wheat plants transformed with WKS1 transcript are resistant to Pst. WKS1 is targeted to the chloroplast where it phosphorylates the thylakoid-associatedascorbateperoxidase (tAPX) and reduces its ability to detoxify peroxides. Based on these results, we propose that the phosphorylation of tAPX by WKS1 reduces the ability of the cells to detoxify ROS and contributes to cell death. Distribution and diversity of WKS in wild emmer populations. We have shown that WKS1 is present only in the southern distribution range of wild emmer in the Fertile Crescent. Sequence analysis revealed a high level of WKS1 conservation among wild emmer populations, in contrast to the high level of diversity observed in NB-LRR genes. This phenomenon shed some light on the evolution of genes that confer partial resistance to Pst. Three new WKS1 haplotypes displayed a resistance response, suggesting that they can be useful to improve wheat resistance to Pst. In summary, we have improved our understanding of cereals’ resistance mechanisms to rusts and we have used that knowledge to develop improved wheat varieties.
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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.
Full textAbstract:
Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.
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Guy, Charles, Gozal Ben-Hayyim, Gloria Moore, Doron Holland, and Yuval Eshdat. Common Mechanisms of Response to the Stresses of High Salinity and Low Temperature and Genetic Mapping of Stress Tolerance Loci in Citrus. United States Department of Agriculture, May 1995. http://dx.doi.org/10.32747/1995.7613013.bard.
Full textAbstract:
The objectives that were outlined in our original proposal have largely been achieved or will be so by the end of the project in February 1995 with one exception; that of mapping cold tolerance loci based on the segregation of tolerance in the BC1 progeny population. Briefly, our goals were to 1) construct a densely populated linkage map of the citrus genome: 2) map loci important in cold and/or salt stress tolerance; and 3) characterize the expression of genes responsive to cold land salt stress. As can be seen by the preceding listing of accomplishments, our original objectives A and B have been realized, objective C has been partially tested, objective D has been completed, and work on objectives E and F will be completed by the end of 1995. Although we have yet to map any loci that contribute to an ability of citrus to maintain growth when irrigated with saline water, our very encouraging results from the 1993 experiment provides us with considerable hope that 1994's much more comprehensive and better controlled experiment will yield the desired results once the data has been fully analyzed. Part of our optimism derives from the findings that loci for growth are closely linked with loci associated with foliar Cl- and Na+ accumulation patterns under non-salinization conditions. In the 1994 experiment, if ion exclusion or sequestration traits are segregating in the population, the experimental design will permit their resolution. Our fortunes with respect to cold tolerance is another situation. In three attempts to quantitatively characterize cold tolerance as an LT50, the results have been too variable and the incremental differences between sensitive and tolerant too small to use for mapping. To adequately determine the LT50 requires many plants, many more than we have been able to generate in the time and space available by making cuttings from small greenhouse-grown stock plants. As it has turned out, with citrus, to prepare enough plants needed to be successful in this objective would have required extensive facilities for both growing and testing hardiness which simply were not available at University of Florida. The large populations necessary to overcome the variability we encountered was unanticipated and unforeseeable at the project's outset. In spite of the setbacks, this project, when it is finally complete will be exceedingly successful. Listing of Accomplishments During the funded interval we have accomplished the following objectives: Developed a reasonably high density linkage map for citrus - mapped the loci for two cold responsive genes that were cloned from Poncirus - mapped the loci for csa, the salt responsive gene for glutathione peroxidase, and ccr a circadian rhythm gene from citrus - identified loci that confer parental derived specific DNA methylation patterns in the Citrus X Poncirus cross - mapped 5 loci that determine shoot vigor - mapped 2 loci that influence leaf Na+ accumulation patterns under non-saline conditions in the BC1 population - mapped 3 loci that influence leaf Na+ accumulation paterns during salt sress - mapped 2 loci that control leaf Cl- accumulation patterns under non-saline conditions - mapped a locus that controls leaf Cl- accumulation patterns during salt stress Screened the BC1 population for growth reduction during salinization (controls and salinized), and cold tolerance - determined population variation for shoot/root ratio of Na+ and Cl- - determined levels for 12 inorganic nutrient elements in an effort to examine the influence of salinization on ion content with emphasis on foliar responses - collected data on ion distribution to reveal patterns of exclusion/sequestration/ accumulation - analyzed relationships between ion content and growth Characterization of gene expression in response to salt or cold stress - cloned the gene for the salt responsive protein csa, identified it as glutathione peroxidase, determined the potential target substrate from enzymatic studies - cloned two other genes responsive to salt stress, one for the citrus homologue of a Lea5, and the other for an "oleosin" like gene - cold regulated (cor) genes belonging to five hybridization classes were isolated from Poncirus, two belonged to the group 2 Lea superfamily of stress proteins, the others show no significant homology to other known sequences - the expression of csa during cold acclimation was examined, and the expression of some of the cor genes were examined in response to salt stress - the influence of salinization on cold tolerance has been examined with seedling populations - conducted protein blot studies for expression of cold stress proteins during salt stress and vice versa
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Zamir, Dani, Steven Tanksley, and Robert Fluhr. Cloning a Fusarium Resistance Gene in Tomato Based on Knowledge of its Map Position. United States Department of Agriculture, July 1995. http://dx.doi.org/10.32747/1995.7604934.bard.
Full textAbstract:
The objectives of this project were to develop the tools and methodologies for positional cloning of genes in tomato and apply them for the cloning a Fusarium resistance gene - I2.. The feasibility of positional cloning of disease resistance genes was demonstrated for Pto which confers resistance to pseudomonas (Martin et al. 1993). The Fusarium resistance gene was mapped genetically and physically and was found to be in close proximity to TG 105 (Segal et al. 1992). To obtain fine mapping of gene I2, and additional target genes in future projects, a high density linkage map was developed (Tanksley et al. 1992; Broun and Tanksley 1993). In addition two permanent mapping populations were constructed: a recombinant inbred (Paran et al. 1995; Zamir et al. 1993) and an introgression line population (Eshed et al. 1992; Eshed and Zamir 1994). Using these resources we determined that the I2 locus shows complete co-segregation, down to a resolution of a few Kb, with SL8 which shows architectural similarity with other plant resistance genes. Transformation and complementation analysis is in progress (Ori et al. in preparation).
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Hovav, Ran, Peggy Ozias-Akins, and Scott A. Jackson. The genetics of pod-filling in peanut under water-limiting conditions. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597923.bard.
Full textAbstract:
Pod-filling, an important yield-determining stage is strongly influenced by water stress. This is particularly true for peanut (Arachishypogaea), wherein pods are developed underground and are directly affected by the water condition. Pod-filling in peanut has a significant genetic component as well, since genotypes are considerably varied in their pod-fill (PF) and seed-fill (SF) potential. The goals of this research were to: Examine the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Detect global changes in mRNA and metabolites levels that accompany PF and SF. Explore the response of the duplicate peanut pod transcriptome to drought stress. Study how entire duplicated PF regulatory processes are networked within a polyploid organism. Discover locus-specific SNP markers and map pod quality traits under different environments. The research included genotypes and segregating populations from Israel and US that are varied in PF, SF and their tolerance to water deficit. Initially, an extensive field trial was conducted to investigate the effects of genotype, irrigation, and genotype X irrigation on PF and SF. Significant irrigation and genotypic effect was observed for the two main PF related traits, "seed ratio" and "dead-end ratio", demonstrating that reduction in irrigation directly influences the developing pods as a result of low water potential. Although the Irrigation × Genotype interaction was not statistically significant, one genotype (line 53) was found to be more sensitive to low irrigation treatments. Two RNAseq studies were simultaneously conducted in IL and the USA to characterize expression changes that accompany shell ("source") and seed ("sink") biogenesis in peanut. Both studies showed that SF and PF processes are very dynamic and undergo very rapid change in the accumulation of RNA, nutrients, and oil. Some genotypes differ in transcript accumulation rates, which can explain their difference in SF and PF potential; like cvHanoch that was found to be more enriched than line 53 in processes involving the generation of metabolites and energy at the beginning of seed development. Interestingly, an opposite situation was found in pericarp development, wherein rapid cell wall maturation processes were up-regulated in line 53. Although no significant effect was found for the irrigation level on seed transcriptome in general, and particularly on subgenomic assignment (that was found almost comparable to a 1:1 for A- and B- subgenomes), more specific homoeologous expression changes associated with particular biosynthesis pathways were found. For example, some significant A- and B- biases were observed in particular parts of the oil related gene expression network and several candidate genes with potential influence on oil content and SF were further examined. Substation achievement of the current program was the development and application of new SNP detection and mapping methods for peanut. Two major efforts on this direction were performed. In IL, a GBS approach was developed to map pod quality traits on Hanoch X 53 F2/F3 generations. Although the GBS approach was found to be less effective for our genetic system, it still succeeded to find significant mapping locations for several traits like testa color (linkage A10), number of seeds/pods (A5) and pod wart resistance (B7). In the USA, a SNP array was developed and applied for peanut, which is based on whole genome re-sequencing of 20 genotypes. This chip was used to map pod quality related traits in a Tifrunner x NC3033 RIL population. It was phenotyped for three years, including a new x-ray method to phenotype seed-fill and seed density. The total map size was 1229.7 cM with 1320 markers assigned. Based on this linkage map, 21 QTLs were identified for the traits 16/64 weight, kernel percentage, seed and pod weight, double pod and pod area. Collectively, this research serves as the first fundamental effort in peanut for understanding the PF and SF components, as a whole, and as influenced by the irrigation level. Results of the proposed study will also generate information and materials that will benefit peanut breeding by facilitating selection for reduced linkage drag during introgression of disease resistance traits into elite cultivars. BARD Report - Project4540 Page 2 of 10
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Bennett, Alan B., Arthur A. Schaffer, Ilan Levin, Marina Petreikov, and Adi Doron-Faigenboim. Manipulating fruit chloroplasts as a strategy to improve fruit quality. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598148.bard.
Full textAbstract:
The Original Objectives were modified and two were eliminated to reflect the experimental results: Objective 1 - Identify additional genetic variability in SlGLK2 and IPin wild, traditional and heirloom tomato varieties Objective 2 - Determine carbon balance and horticultural characteristics of isogenic lines expressing functional and non-functional alleles of GLKsand IP Background: The goal of the research was to understand the unique aspects of chloroplasts and photosynthesis in green fruit and the consequences of increasing the chloroplast capacity of green fruit for ripe fruit sugars, yield, flavor and nutrient qualities. By focusing on the regulation of chloroplast formation and development solely in fruit, our integrated knowledge of photosynthetic structures/organs could be broadened and the results of the work could impact the design of manipulations to optimize quality outputs for the agricultural fruit with enhanced sugars, nutrients and flavors. The project was based on the hypothesis that photosynthetic and non-photosynthetic plastid metabolism in green tomato fruit is controlled at a basal level by light for minimal energy requirements but fruit-specific genes regulate further development of robust chloroplasts in this organ. Our BARD project goals were to characterize and quantitate the photosynthesis and chloroplast derived products impacted by expression of a tomato Golden 2- like 2 transcription factor (US activities) in a diverse set of 31 heirloom tomato lines and examine the role of another potential regulator, the product of the Intense Pigment gene (IP activities). Using tomato Golden 2-like 2 and Intense Pigment, which was an undefined locus that leads to enhanced chloroplast development in green fruit, we sought to determine the benefits and costs of extensive chloroplast development in fruit prior to ripening. Major conclusions, solutions, achievements: Single nucleotide polymorphisms in the promoter, coding and intronicSlGLK2 sequences of 20 heirloom tomato lines were identified and three SlGLK2 promoter lineages were identified; two lineages also had striped fruit variants. Lines with striped fruit but no shoulders were not identified. Green fruit chlorophyll and ripe fruit soluble sugar levels were measured in 31 heirloom varieties and fruit size correlates with ripe fruit sugars but dark shoulders does not. A combination of fine mapping, recombinant generation, RNAseq expression and SNP calling all indicated that the proposed localization of a single locus IP on chr 10 was incorrect. Rather, the IP line harbored 11 separate introgressions from the S. chmielewskiparent, scattered throughout the genome. These introgressions harbored ~3% of the wild species genome and no recombinant consistently recovered the IP parental phenotype. The 11 introgressions were dissected into small combinations in segregating recombinant populations. Based on these analyses two QTL for Brix content were identified, accounting for the effect of increased Brix in the IP line. Scientific and agricultural implications: SlGLK2 sequence variation in heirloom tomato varieties has been identified and can be used to breed for differences in SlGLK2 expression and possibly in the green striped fruit phenotype. Two QTL for Brix content have been identified in the S. chmielewskiparental line and these can be used for increasing soluble solids contents in breeding programs.