棉花PHYA、PHYB和HY5特异性CAPS及dCAPS标记的开发、遗传图谱构建与QTL关联分析
Development, genetic mapping and QTL association of cotton PHYA, PHYB, and HY5-specific CAPS and dCAPS markers.
作者信息
Kushanov Fakhriddin N, Pepper Alan E, Yu John Z, Buriev Zabardast T, Shermatov Shukhrat E, Saha Sukumar, Ulloa Mauricio, Jenkins Johnie N, Abdukarimov Abdusattor, Abdurakhmonov Ibrokhim Y
机构信息
Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, University Street-2, Qibray region, Tashkent District, 111215, Uzbekistan.
Department of Biology, Texas A&M University, Colleges Station, TX, 77843, USA.
出版信息
BMC Genet. 2016 Oct 24;17(1):141. doi: 10.1186/s12863-016-0448-4.
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 (AD and AD) when tested in parental genotypes of 'Texas Marker-1' ('TM-1'), 'Pima 3-79' and their F 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.
背景
在作物分子育种中变得越来越有价值的单核苷酸多态性（SNP）标记中，有来源于目标基因的酶切扩增多态性序列（CAPS）和衍生酶切扩增多态性序列（dCAPS）标记。迄今为止，在具有A和D亚基因组的多倍体作物如异源四倍体棉花中，这类基于基因的标记数量很少。本研究的目的是开发并定位对植物育种计划很重要的棉花发育调控基因的新CAPS和dCAPS标记。
结果
陆地棉和海岛棉是两种栽培的异源四倍体棉花物种。它们具有不同的纤维品质和其他农艺性状。通过对陆地棉和海岛棉的PHYA1、PHYB和HY5基因的已鉴定谷胱甘肽S-转移酶（GST）进行比较序列分析，开发了一个PHYA1特异性的Mbo I/Dpn II CAPS、一个PHYB特异性的Alu I dCAPS和一个HY5特异性的Hinf I dCAPS棉花标记。当在‘德州标记-1’（‘TM-1’）、‘皮马3-79’及其F1杂种的亲本基因型中进行测试时，这些标记成功地区分了两个异源四倍体基因组（AD1和AD2）。基于遗传图谱绘制和染色体代换系的缺失分析表明，在参考的‘TM-1’ב皮马3-79’重组自交系（RIL）遗传图谱上，PHYA1基因位于A亚基因组的第11号染色体上，PHYB基因位于A亚基因组的第10号染色体上，HY5基因位于D亚基因组的第24号染色体上。此外，发现在先前发表的数量性状基因座（QTL）定位研究中，包含光敏色素和HY5特异性标记的遗传连锁图谱区域与主要纤维品质和开花时间性状相关。
结论
本研究详细阐述了利用新开发的CAPS和dCAPS标记对三个棉花光敏色素基因进行基因组定位。在两个A亚基因组和一个D亚基因组染色体中证明了这些基因座与纤维品质和其他棉花QTL的接近性。这些候选基因标记对于标记辅助选择（MAS）计划将非常有价值，该计划可将海岛棉光敏色素和/或HY5基因快速导入陆地棉基因型中，反之亦然。
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