Mohammed Jamal, Thyssen Gregory N, Hinze Lori, Zhang Jinfa, Zeng Linghe, Fang David D
Cotton Fiber Bioscience and Utilization Research Unit, USDA-ARS-SRRC, New Orleans, 70124, LA, USA.
Crop Germplasm Research Unit, USDA-ARS, College Station, 77845, TX, USA.
Theor Appl Genet. 2024 Dec 23;138(1):10. doi: 10.1007/s00122-024-04800-z.
GWAS of a new MAGIC population containing alleles from five tetraploid Gossypium species identified novel fiber QTL and confirmed previously identified stable QTL. Identification of loci and underlying genes for fiber quality traits will facilitate genetic improvement in cotton fiber quality. In this research, a genome-wide association study (GWAS) was carried out for fiber quality attributes using a new multi-parent advanced generation inter-cross (MAGIC) population consisting of 372 recombinant inbred lines (RILs). Sixteen parents including 12 exotic germplasm lines derived from five tetraploid Gossypium species and 4 Upland cotton varieties were intercrossed to develop the population. Both RILs and parental lines were evaluated at three locations, College Station, Texas; Las Cruses, New Mexico; and Stoneville, Mississippi, from 2016 through 2023. Fiber length (UHM) had positive correlation with strength (STR) and length uniformity (UNI) and a negative correlation with micronaire (MIC) and elongation (ELO). By combining all the data from all locations, we identified significant SNPs for ELO, UHM, and UNI while STR and MIC were location dependent. These results suggest an important role of genotype by environment interaction in a GWAS of fiber traits. Twenty possible novel fiber QTL were identified: 10 for STR, three for UNI, and seven for MIC. The QTL for ELO (Chr.D04: 53-Mb), UHM (Chr.D11: 24-Mb), and UNI (Chr.D04: 34-Mb) were stable across multiple environments and may be useful for marker-assisted selection to improve fiber quality. For STR, we found candidate genes Gh_A07G1574 and Gh_A07G1581 to be present in the previously identified QTL region (Chr.A07: 77-Mb) on chromosome A07. Identified loci and their corresponding candidate genes will be useful to improve fiber quality via marker-assisted selection in a cotton breeding.
对一个包含来自五个四倍体棉种等位基因的新型多亲本高级世代杂交（MAGIC）群体进行全基因组关联研究（GWAS），鉴定出了新的纤维数量性状位点（QTL），并证实了先前鉴定出的稳定QTL。鉴定纤维品质性状的位点和潜在基因将有助于棉花纤维品质的遗传改良。在本研究中，利用一个由372个重组自交系（RIL）组成的新型多亲本高级世代杂交（MAGIC）群体，对纤维品质属性进行了全基因组关联研究（GWAS）。该群体由16个亲本杂交培育而成，其中包括来自五个四倍体棉种的12个外来种质系和4个陆地棉品种。从2016年到2023年，RIL和亲本系在德克萨斯州的大学站、新墨西哥州的拉斯克鲁塞斯和密西西比州的斯通维尔三个地点进行了评估。纤维长度（UHM）与强度（STR）和长度均匀度（UNI）呈正相关，与马克隆值（MIC）和伸长率（ELO）呈负相关。通过整合所有地点的所有数据，我们鉴定出了与ELO、UHM和UNI显著相关的单核苷酸多态性（SNP），而STR和MIC则依赖于地点。这些结果表明基因型与环境互作在纤维性状的GWAS中起着重要作用。鉴定出了20个可能的新型纤维QTL：10个与STR相关，3个与UNI相关，7个与MIC相关。ELO（Chr.D04: 53-Mb）、UHM（Chr.D11: 24-Mb）和UNI（Chr.D04: 34-Mb）的QTL在多个环境中都很稳定，可能有助于标记辅助选择以提高纤维品质。对于STR，我们发现候选基因Gh_A07G1574和Gh_A07G1581存在于先前在A07染色体上鉴定出的QTL区域（Chr.A07: 77-Mb）中。鉴定出的位点及其相应的候选基因将有助于通过棉花育种中的标记辅助选择来提高纤维品质。
