Liu Yingfei, Nazir Mian Faisal, He Shoupu, Li Hongge, Pan Zhaoe, Sun Gaofei, Dai Panhong, Wang Liyuan, Du Xiongming
Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China.
Theor Appl Genet. 2022 Apr;135(4):1401-1411. doi: 10.1007/s00122-022-04042-x. Epub 2022 Feb 10.
Foundation parents play a critical role in the genetic constituents of the derived genotypes. Deltapine-15 (DLP-15), introduced to China in 1950, is one of the most commonly used parents for early breeding programs in China. However, the formation and inheritance patterns of genomic constituents have not been studied. Therefore, this study aimed at understanding and exploring the genomic architecture of 146 DLP-15 derived cultivars with a common foundation parent DLP-15. Population structure based on sequencing data clustered genotypes into two groups (G1 and G2) supported by principal component analysis. Further exploration led to the identification of Chr-A08 with significantly differentiated regions between two groups. Moreover, we identified genome-wide identity by descent (IBD) segments (840 segments) to understand the genomic inheritance pattern in DLP-15 derived cultivars, spanning the 20-95 Mb region on Chr-A08. Interestingly, Chr-A08 depicted a unique inheritance pattern from DLP-15 to its derived cultivars. IBD-segment-based haplotype analysis suggested significant differences among the two groups. Phenotypic trait association with DLP-derived haplotypes concerning Chr-A08 suggested a significant increase in yield and fiber quality. Furthermore, distinguished IBD segments overlapped with previously reported QTLs concerning fiber yield and quality. Our results systematically identified genomic signatures transmitted from the foundation parent DLP-15 to its derived cultivars and provided a basis for further exploiting excellent haplotypes associated with DLP-15.
基础亲本在衍生基因型的遗传组成中起着关键作用。1950年引入中国的岱字棉15号(DLP - 15)是中国早期育种项目中最常用的亲本之一。然而,其基因组组成的形成和遗传模式尚未得到研究。因此,本研究旨在了解和探索146个以共同基础亲本DLP - 15衍生的品种的基因组结构。基于测序数据的群体结构将基因型聚类为两组(G1和G2),主成分分析也支持这一结果。进一步探索发现了Chr - A08上两组之间存在显著差异的区域。此外,我们鉴定了全基因组的同源片段(IBD)(840个片段),以了解DLP - 15衍生品种的基因组遗传模式,这些片段跨越了Chr - A08上20 - 95 Mb的区域。有趣的是,Chr - A08呈现出从DLP - 15到其衍生品种的独特遗传模式。基于IBD片段的单倍型分析表明两组之间存在显著差异。与Chr - A08的DLP衍生单倍型相关的表型性状关联表明产量和纤维品质显著提高。此外,区分出的IBD片段与先前报道的有关纤维产量和品质的QTL重叠。我们的结果系统地鉴定了从基础亲本DLP - 15传递到其衍生品种的基因组特征,并为进一步开发与DLP - 15相关的优良单倍型提供了基础。