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

Fakhriddin N Kushanov; Alan E Pepper; John Z Yu; Zabardast T Buriev; Shukhrat E Shermatov; Sukumar Saha; Mauricio Ulloa; Johnie N Jenkins; Abdusattor Abdukarimov; Ibrokhim Y Abdurakhmonov

doi:10.1186/s12863-016-0448-4

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

BMC Genet. 2016 Oct 24;17(1):141. doi: 10.1186/s12863-016-0448-4.

Affiliations

¹ Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region, Tashkent District, 111215, Uzbekistan.
² Department of Biology, Texas A&M University, Colleges Station, TX, 77843, USA.
³ USDA-ARS, Southern Plains Agricultural Research Center, 2881 F&B Road, College Station, TX, 77845, USA.
⁴ USDA-ARS, Crop Science Research Laboratory, Mississippi State, MS, 39762, USA.
⁵ USDA-ARS, Plant Stress and Germplasm Development Research, 3810 4th Street, Lubbock, TX, 79415, USA.
⁶ Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region, Tashkent District, 111215, Uzbekistan. ibrokhim.abdurakhmonov@genomics.uz.

Abstract

Background: Among SNP markers that become increasingly valuable in molecular breeding of crop plants are the CAPS and dCAPS markers derived from the genes of interest. To date, the number of such gene-based markers is small in polyploid crop plants such as allotetraploid cotton that has A- and D-sub-genomes. The objective of this study was to develop and map new CAPS and dCAPS markers for cotton developmental-regulatory genes that are important in plant breeding programs.

Results: Gossypium hirsutum and G. barbadense, are the two cultivated allotetraploid cotton species. These have distinct fiber quality and other agronomic traits. Using comparative sequence analysis of characterized GSTs of the PHYA1, PHYB, and HY5 genes of G. hirsutum and G. barbadense one PHYA1-specific Mbo I/Dpn II CAPS, one PHYB-specific Alu I dCAPS, and one HY5-specific Hinf I dCAPS cotton markers were developed. 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. The genetic mapping and chromosome substitution line-based deletion analyses revealed that PHYA1 gene is located in A-sub-genome chromosome 11, PHYB gene is in A-sub-genome chromosome 10, and HY5 gene is in D-sub-genome chromosome 24, on the reference 'TM-1' x 'Pima 3-79' RIL genetic map. Further, it was found that genetic linkage map regions containing phytochrome and HY5-specific markers were associated with major fiber quality and flowering time traits in previously published QTL mapping studies.

Conclusion: This study detailed the genome mapping of three cotton phytochrome genes with newly developed CAPS and dCAPS markers. The proximity of these loci to fiber quality and other cotton QTL was demonstrated in two A-subgenome and one D-subgenome chromosomes. These candidate gene markers will be valuable for marker-assisted selection (MAS) programs to rapidly introgress G. barbadense phytochromes and/or HY5 gene (s) into G. hirsutum cotton genotypes or vice versa.

Keywords: CAPS and dCAPS; Cotton; Fiber QTLs; Linkage mapping; Phytochromes.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosome Mapping*
Genes, Plant*
Genetic Linkage
Genetic Markers
Genome, Plant*
Genomics* / methods
Gossypium / genetics*
Gossypium / metabolism
Phytochrome
Quantitative Trait Loci*
Quantitative Trait, Heritable

Substances

Genetic Markers
Phytochrome