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Genomic Variation Mapping and Detection of Novel Genes Based on Genome-Wide Survey of an Elite Upland Cotton Hybrid (Gossypium hirsutum L.)


Affiliations
1 State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
2 College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
 

CCRI63, with the largest cultivated area among hybrids in China, is a successful promotion of elite up-land cotton (Gossypium hirsutum L.) hybrid cultivar. We have constructed a detailed genomic variation map of CCRI63 by aligning whole-genome shotgun sequencing reads from CCRI63 to the TM-1 reference genome. Genomic single nucleotide poly-morphism (SNP) and insertion-deletion (Indel) muta-tional hotspots were identified, most of which were located on chromosome D02, and associated with dis-ease resistance and lipid glycosylation and modification. The density of heterozygous SNP sites showed 73 quantitative trait loci overlapped with peak intervals of high-density heterozygous SNPs, suggesting that the heterozygous sites in the peak are important for improvement of CCRI63 yield and fibre quality. To avoid loss of genetic components, unmapped reads were used for de novo assembly of the missing regions in the reference genome, and 153 novel functional genes were obtained. The large-scale genetic variation and novel functional genes identified in the CCRI63 genome can facilitate future gene-phenotype studies and provide an additional resource for the improvement of cotton.

Keywords

Cotton Hybrid, Genomic Variation Map, Mutational Hotspots, Novel Genes.
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  • Genomic Variation Mapping and Detection of Novel Genes Based on Genome-Wide Survey of an Elite Upland Cotton Hybrid (Gossypium hirsutum L.)

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Authors

Zhenyu Wang
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Wei Li
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Guanghui Xiao
College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
Xiaojian Zhou
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Xiaoyu Pei
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Yangai Liu
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Kehai Zhou
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Kunlun He
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Junfang Liu
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Ying Li
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Wensheng Zhang
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Zhongying Ren
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Qingqin Meng
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Haifeng Wang
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Xiongfeng Ma
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
Daigang Yang
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China

Abstract


CCRI63, with the largest cultivated area among hybrids in China, is a successful promotion of elite up-land cotton (Gossypium hirsutum L.) hybrid cultivar. We have constructed a detailed genomic variation map of CCRI63 by aligning whole-genome shotgun sequencing reads from CCRI63 to the TM-1 reference genome. Genomic single nucleotide poly-morphism (SNP) and insertion-deletion (Indel) muta-tional hotspots were identified, most of which were located on chromosome D02, and associated with dis-ease resistance and lipid glycosylation and modification. The density of heterozygous SNP sites showed 73 quantitative trait loci overlapped with peak intervals of high-density heterozygous SNPs, suggesting that the heterozygous sites in the peak are important for improvement of CCRI63 yield and fibre quality. To avoid loss of genetic components, unmapped reads were used for de novo assembly of the missing regions in the reference genome, and 153 novel functional genes were obtained. The large-scale genetic variation and novel functional genes identified in the CCRI63 genome can facilitate future gene-phenotype studies and provide an additional resource for the improvement of cotton.

Keywords


Cotton Hybrid, Genomic Variation Map, Mutational Hotspots, Novel Genes.

References





DOI: https://doi.org/10.18520/cs%2Fv115%2Fi4%2F701-709