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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 #330594

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

Location: Crop Germplasm Research

Title: Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers

Author
item Kushanov, Fakhriddin - Uzbekistan Academy Of Sciences
item Pepper, Alan - Texas A&M University
item Yu, John
item Buriev, Zabardast - Uzbekistan Academy Of Sciences
item Shermatov, Shukhrat - Uzbekistan Academy Of Sciences
item Saha, Sukumar
item Ulloa, Mauricio
item Jenkins, Johnie
item Abdukarimov, Abdusattor - Uzbekistan Academy Of Sciences
item Abdurakhmonov, Ibrokhim - Uzbekistan Academy Of Sciences

Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/11/2016
Publication Date: 10/24/2016
Citation: Kushanov, F.N., Pepper, A.E., Yu, J., Buriev, Z.T., Shermatov, S.E., Saha, S., Ulloa, M., Jenkins, J.N., Abdukarimov, A., Abdurakhmonov, I.Y. 2016. Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers. BioMed Central (BMC) Genetics. 17:141.

Interpretive Summary: DNA markers derived from the genes of interest become increasingly valuable in molecular breeding of crop plants. The number of available gene-based markers is small for crop plants such as cotton. Much of the limitation is due to the polyploidy of most crop plants such as Upland cotton that has two subgenomes called A and D. In this study, we developed and mapped three gene-based markers called cleaved amplified polymorphism (CAP) from phytochrome and flowering genes in cotton. Two phytochrome genes were located in chromosomes 10 and 11, respectively, of A-subgenome. One flowering gene was located in chromosome 24 of D-subgenome. The association of these gene-based markers to fiber quality and other cotton traits with many additional DNA markers was also demonstrated in the three cotton chromosomes. The new markers developed and mapped in this study are of particular value to differentiate DNA polymorphisms from only single subgenome of polyploid species, giving an opportunity to analyze a polyploid as a diploid genotype. These gene-based markers would be highly useful for marker-assisted selection (MAS) programs to breed superior cotton cultivars by introgression of phytochrome and flowering genes among different cotton species.

Technical Abstract: Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAP and dCAP markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as tetraploid cotton that has A and D subgenomes. The objective of this study was to develop and map new CAP and dCAP markers for cotton phytochrome genes that are important in plant breeding programs. Using comparative sequence analysis of characterized GSTs PHYA1, PHYB, and HY5 genes of G. hirsutum and G. barabadense, only two allotetraploid cotton species cultivated worldwide with distinct fiber quality and other agronomic traits, we developed one PHYA1-specific Mbo I/Dpn II CAPs, one PHYB-specific Alu I dCAPs, and one HY5-specific Hinf I dCAPs cotton markers. These markers have successfully differentiated the two allotetraploid genomes (AD1 and AD2) when tested in parental genotypes of Texas Marker-1 (TM-1), Pima-3-79 and their F1 hybrids. Our genetic mapping analyses revealed that PHYA1 gene is located in A-subgenome chromosome 11, PHYB gene is in A-subgenome chromosome 10, and HY5 gene is in D-subgenome chromosome 24, on the reference TM-1 x 3-79 RIL genetic map. Further, we found that genetic linkage map regions containing phytochrome and HY5-specific markers, flanked with SSR markers, were associated with major fiber quality traits as well as flowering time in various previously published QTL mapping studies. This study detailed the genome mapping of three cotton phytochrome genes with newly CAP and dCAP markers. The proximity of these loci to fiber quality and other cotton traits was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers would be valuable for marker-assisted selection (MAS) programs to rapidly introgress Sea Island phytochrome and/or HY5 gene(s) into Upland cotton genotypes or vice versa.