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

Publication Overview
TitleDevelopment, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers
AuthorsKushanov FN, Pepper AE, Yu JZ, Buriev ZT, Shermatov SE, Saha S, Ulloa M, Jenkins JN, Abdukarimov A, Abdurakhmonov IY
TypeJournal Article
Journal NameBMC genetics
Volume17
Issue1
Year2016
Page(s)141
CitationKushanov FN, Pepper AE, Yu JZ, Buriev ZT, Shermatov SE, Saha S, Ulloa M, Jenkins JN, Abdukarimov A, Abdurakhmonov IY. Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers. BMC genetics. 2016 Oct 24; 17(1):141.

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.

Features
This publication contains information about 4 features:
Feature NameUniquenameType
GhHY5-2_dCAPSGhHY5-2_dCAPSgenetic_marker
PHYA1_CAPSPHYA1_CAPSgenetic_marker
PHYB_dCAPSPHYB_dCAPSgenetic_marker
PHYB_dCAPS-2PHYB_dCAPS-2genetic_marker
Properties
Additional details for this publication include:
Property NameValue
eISSN1471-2156
Publication Date2016 Oct 24
Journal AbbreviationBMC Genet.
ISSN1471-2156
Publication ModelElectronic
LanguageEnglish
Language AbbrENG
Publication TypeJournal Article
Journal CountryEngland