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Resequencing of 388 cassava accessions identifies valuable loci and selection for variation in heterozygosity

文献类型： 外文期刊

作者： Hu, Wei 1 ; Ji, Changmian 1 ; Liang, Zhe 4 ; Ye, Jianqiu 5 ; Ou, Wenjun 5 ; Ding, Zehong 1 ; Zhou, Gang 6 ; Tie, Weiwei 1 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Sanya Res Inst, Sanya, Hainan, Peoples R China

2.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Hainan Key Lab Biosafety Monitoring & Mol Breedin, Key Lab Biol & Genet Resources Trop Crops, Haikou, Hainan, Peoples R China

3.Chinese Acad Trop Agr Sci, Hainan Inst Trop Agr Resources, Hainan Key Lab Protect & Utilizat Trop Bioresourc, Haikou, Hainan, Peoples R China

4.Chinese Acad Agr Sci, Biotechnol Res Inst, Beijing, Peoples R China

5.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Haikou, Hainan, Peoples R China

6.Biomarker Technol Corp, Beijing, Peoples R China

7.Qilu Univ Technol, Coll Food Sci & Technol, Shandong Acad Sci, Jinan, Peoples R China

8.Hainan Univ, Coll Trop Crops, Hainan Key Lab Sustainable Utilizat Trop Bioresou, Haikou, Hainan, Peoples R China

9.Columbia Univ, Fu Fdn Sch Engn & Appl Sci, New York, NY 10027 USA

10.Rutgers State Univ, Waksman Inst Microbiol, Piscataway, NJ USA

11.Fujian Agr & Forestry Univ, Key Lab Genet Breeding & Multiple Utilizat Crops, Fujian Prov Key Lab Haixia Appl Plant Syst Biol, FAFU & UIUC SIB Joint Ctr Genom & Biotechnol,Mini, Fuzhou, Peoples R China

12.Univ Illinois, Dept Plant Biol, Urbana, IL 61820 USA

关键词： Resequencing; Cassava; Heterozygosity; Selection; Agronomic traits

期刊名称：GENOME BIOLOGY （ 影响因子：13.583； 五年影响因子：17.433 ）

ISSN： 1474-760X

年卷期： 2021 年 22 卷 1 期

页码：

收录情况： SCI

摘要： Background Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassava is a staple crop in Africa and other tropical regions and has a highly heterozygous genome. Results We describe a genomic variation map from 388 resequenced genomes of cassava cultivars and wild accessions. We identify 52 loci for 23 agronomic traits through a genome-wide association study. Eighteen allelic variations in heterozygosity for nine candidate genes are significantly associated with seven key agronomic traits. We detect 81 selective sweeps with decreasing heterozygosity and nucleotide diversity, harboring 548 genes, which are enriched in multiple biological processes including growth, development, hormone metabolisms and responses, and immune-related processes. Artificial selection for decreased heterozygosity has contributed to the domestication of the large starchy storage root of cassava. Selection for homozygous GG allele in MeTIR1 during domestication contributes to increased starch content. Selection of homozygous AA allele in MeAHL17 is associated with increased storage root weight and cassava bacterial blight (CBB) susceptibility. We have verified the positive roles of MeTIR1 in increasing starch content and MeAHL17 in resistance to CBB by transient overexpression and silencing analysis. The allelic combinations in MeTIR1 and MeAHL17 may result in high starch content and resistance to CBB. Conclusions This study provides insights into allelic variation in heterozygosity associated with key agronomic traits and cassava domestication. It also offers valuable resources for the improvement of cassava and other highly heterozygous crops.

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