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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #299076

Research Project: Developing Genomic and Genetic Tools for Exploiting Cotton Genetic Variation

Location: Crop Germplasm Research

Title: Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. x G. barbadense L.) RIL population

item Yu, John
item Ulloa, Mauricio
item HOFFMAN, STEVEN - Texas A&M University
item Kohel, Russell
item PEPPER, ALAN - Texas A&M University
item Fang, David
item Percy, Richard
item Burke, John

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/20/2014
Publication Date: 11/18/2014
Citation: Yu, J., Ulloa, M., Hoffman, S.M., Kohel, R.J., Pepper, A.E., Fang, D.D., Percy, R.G., Burke, J.J. 2014. Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. x G. barbadense L.) RIL population. Molecular Genetics and Genomics. 289:1347-1367.

Interpretive Summary: Understanding of genetic variation that confers plant growth and fiber yield and quality is essential for cotton improvement. However, most of these traits are quantitatively inherited and are conferred by multiple genes located in different parts of the cotton genome. With our recent development of a high-density genetic map of 2,500 molecular markers, we analyzed the phenotypic data of 24 morphological, yield, and fiber traits that were collected from an inter-specific mapping population of 186 recombinant inbred lines (RILs) grown in three diverse environments. We identified 383 putative loci that were mapped in 159 genomic regions, of which 75 loci had strong association with phenotypic variation. Several clusters of these loci, called quantitative trait loci (QTL), were discovered in cotton chromosomes. The information gained from this study will help cotton researchers understand and exploit desirable genetic variation for cotton. Molecular markers associated with these QTL clusters will be useful in dissecting genetic factors underlying these traits and in marker-assisted selection to improve the cotton plant with higher yield and better quality of the world's most important natural fiber.

Technical Abstract: A quantitative trait loci (QTL) analysis was conducted to better understand the genetic control of plant architecture (PA), yield components (YC), and fiber properties (FP) in the two cultivated tetraploid species of cotton (Gossypium hirsutum L. and G. barbadense L.). Genomic regions were identified on a saturated genetic map of more than 2,500 SSR and SNP markers constructed using an interspecific RIL population derived from the genetic standards of the respective cotton species (G. hirsutum acc. TM-1 x G. barbadense acc. 3-79). Using the single-nonparametric and MQM QTL model mapping procedures, we detected 383 putative loci and further confirmed 159 genomic regions that confer 24 cotton traits in three diverse environments [College Station F&B Road (FB), TX, Brazos Bottom (BB) TX, and Shafter (SH), CA]. These putative QTL loci included 62 loci for PA, 79 for YC, and 242 for FP, of which3, 12, and 60, respectively, were strongly associated to the traits (LOD score >/= 3.0). Approximately 17.7% of the PA putative QTL, 32.9% of the YC QTL, and 48.3% of the FP QTL had trait associations under multiple environments. The At subgenome (chromosomes 1-13) contributed 72.7% of loci for PA, 46.2% for YC, and 50.4% for FP while the Dt subgenome (chromosomes 14-26) contributed 27.3% of loci for PA, 53.8% for YC, and 49.6% for FP. The data obtained from this study augment prior evidence of QTL clusters or gene islands for specific traits or functions existing in several cotton chromosomes. DNA markers identified in the 159 genomic regions will facilitate further dissection of genetic factors underlying these traits and marker-assisted selection in cotton.