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Jackson, MS, United States

Saha S.,Crop Science Research Laboratory | Wu J.,Mississippi State University | Wu J.,South Dakota State University | Jenkins J.N.,Crop Science Research Laboratory | And 3 more authors.
Theoretical and Applied Genetics

Genetic diversity is the foundation of any cropimprovement program, but the most cultivated Uplandcotton [Gossypium hirsutum L., 2n = 52, genomic formula2(AD)1] has a very narrow gene pool resulting fromits evolutionary origin and domestication history. Cultivarsof this cotton species (G. hirsutum L.) are prized for theircombination of exceptional yield, other agronomic traits,and good fiber properties, whereas the other cultivated52-chromosome species, G. barbadense L. [2n = 52,genomic formula 2(AD)2], is widely regarded as havingthe opposite attributes. It has exceptionally good fiberqualities, but generally lower yield and less desirableagronomic traits. Breeders have long aspired to combinethe best attributes of G. hirsutum and G. barbadense, buthave had limited success. F1 hybrids are readily created andlargely fertile, so the limited success may be due to crypticbiological and technical challenges associated with theconventional methods of interspecific introgression. Wehave developed a complementary alternative approach forintrogression based on chromosome substitution line, followedby increasingly sophisticated genetic analyses ofchromosome-derived families to describe the inheritanceand breeding values of the chromosome substitution lines.Here, we analyze fiber quality traits of progeny familiesfrom a partial diallel crossing scheme among selectedchromosome substitution lines (CS-B lines). The resultsprovide a more detailed and precise QTL dissection of fibertraits, and an opportunity to examine allelic interactioneffects between two substituted chromosomes versus onesubstituted chromosome. This approach creates newgermplasm based on pair wise combinations of quasi-isogenicchromosome substitutions. The relative geneticsimplicity of two-chromosome interactions departs significantlyfrom complex or RIL-based populations, in whichhuge numbers of loci are segregating in all 26 chromosomepairs. Data were analyzed according to the ADAA geneticmodel, which revealed significant additive, dominance, andadditive-by-additive epistasis effects on all of the fiberquality traits associated with the substituted chromosomeor chromosome arm of CS-B lines. Fiber of line 3-79, thedonor parent for the substituted chromosomes, had thehighest Upper Half Mean length (UHM), uniformity ratio,strength, elongation, and lowest micronaire among allparents and hybrids. CS-B16 and CS-B25 had significantadditive effects for all fiber traits. Assuming a uniformgenetic background of the CS-B lines, the comparativeanalysis of the double-heterozygous hybrid combinations(CS-B 9 CS-B) versus their respective single heterozygouscombinations (CS-B 9 TM-1) demonstrated that interspecific epistatic effects between the genes in thechromosomes played a major role in most of the fiberquality traits. Results showed that fiber of several hybridsincluding CS-B16 9 CS-B22Lo, CS-B16 9 CS-B25 andCS-B16 9 TM-1 had significantly greater dominanceeffects for elongation and hybrid CS-B16 9 CS-B17 hadhigher fiber strength than their parental lines. Multipleantagonistic genetic effects were also present for fiberquality traits associated with most of the substituted chromosomesand chromosome arms. Results from this studyhighlight the vital importance of epistasis in fiber qualitytraits and detected novel effects of some cryptic beneficialalleles affecting fiber quality on the 3-79 chromosomes,whose effects were not detected in the 3-79 parental lines. © Springer-Verlag (outside the USA) 2011. Source

Shapulatov U.M.,REPUBLIC RESOURCES | Buriev Z.T.,REPUBLIC RESOURCES | Ulloa M.,Plant Stress and Germplasm Development Research | Saha S.,Crop Science Research Laboratory | And 7 more authors.
Plant Molecular Biology Reporter

Genes for host-plant resistant do exist in cotton (Gossypium spp.) but improvement of cotton cultivars with resistance is difficult due to intensive breeding. Identifying molecular-genetic mechanisms associated with disease resistance can offer a new way to combat a serious threat such as Fusarium oxysporum f. sp. vasinfectum (FOV). Here, we captured and annotated “top-layer” of abundantly and specifically expressed cotton root small RNA (sRNA) including microRNA (miR) sequences during FOV pathogenesis using size-directed and adenylated linker-based sRNA cloning strategy. A total of 4116 candidate sRNA sequences with 16 to 30 nucleotide (nt) length were identified from four complementary DNA (cDNA) libraries of noninfected and FOV race 3-infected roots of susceptible (“11970”) versus resistant (“Mebane B-1”) cotton genotypes (G. hirsutum L.). The highest numbers of sRNA signatures were those with 19–24 nt long in all libraries, and interestingly, the number of sRNAs substantially increased during FOV infection in a resistant genotype, while it sharply decreased in a susceptible genotype. In BLAST analysis, more than 73 % of sRNAs matched Gossypium (G. arboretum L., G. hirsutum, and G. barbadense L.) ESTs. A small percentage of sRNAs matched A. thaliana (1.68 %), T. cacao (1.26 %), fungal (2 %), and other organism (21.33 %) ESTs. mirBase comparisons showed that 4 % of sRNAs were homologous to previously reported plant miRs, among which we predicted novel cotton Ghr-miR-160 that was not registered in the cotton miR database. These major representative sRNA signatures targeted proteins associated with the key biological processes and molecular functions, explaining the molecular mechanisms of the host defense response during the FOV pathogenesis in cotton. © 2015 Springer Science+Business Media New York Source

Bondalapati K.D.,South Dakota State University | Jenkins J.N.,Crop Science Research Laboratory | McCarty J.C.,Crop Science Research Laboratory | Wu J.,South Dakota State University

Field variation is one of the important factors that can have a significant impact on genetic data analysis. Ineffective control of field variation may result in an inflated residual variance and/or biased estimation of genetic variations and/or effects. In this study, we addressed this problem by merging genetic models with the information from a rectangular cotton field layout (referred to row and column directions). Data from a genetic mapping study in Upland cotton (Gossypium hirsutum L.) was used to validate the proposed methodology. This study included model evaluation based on simulations and actual data analysis on four agronomic traits (seed yield, lint yield, lint percentage, and boll weight) in cotton. Results based on simulations suggested that when there were no row and column effects, the conventional and the extended genetic models yielded similar results. However, when either field row and/or column effects were significant, the conventional genetic model yielded biased estimates for residual variance component with larger mean square error whereas the extended genetic models yielded more unbiased estimates. Actual data analysis revealed that lint yield and seed yield were significantly influenced by the systematic variation present in the field. With the extended model, the residual variance associated with these traits was reduced approximately 65 % compared to the conventional block model. Accordingly, the averaged heritability estimate increased by about 18 % for these traits. Thus, the results suggested that genetic data analysis can be improved when field variation is considered. © 2015 Springer Science+Business Media Dordrecht Source

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