Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement.
Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement.
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鹰嘴豆野生祖先 Cicer reticulatum L. 的基因组序列草案为农艺性状改良提供了资源。
DOI：
10.1093/dnares/dsw042
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发表时间：
2017-02-01
期刊：
影响因子：
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通讯作者：
Chattopadhyay D
中科院分区：
文献类型：
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作者：
Gupta S;Nawaz K;Parween S;Roy R;Sahu K;Kumar Pole A;Khandal H;Srivastava R;Kumar Parida S;Chattopadhyay D
鹰嘴豆是第四大豆类作物鹰嘴豆（C. arietinum L.）。我们将短读段序列组装成416 Mb的C.网状结构并将该组装体的78%（327 Mb）锚定到8个连锁群。基因组注释预测了25，680个蛋白质编码基因，覆盖了预测基因空间的90%以上。该基因组组装体与模式豆科植物蒺藜苜蓿基因组在基因序列上具有很强的共线性和保守性。野生和驯化鹰嘴豆的抗病基因同源序列具有高度的同源性和保守的同线性。比较66份野生和驯化鹰嘴豆种质的基因序列和核苷酸多样性表明，德西型鹰嘴豆比卡布里型鹰嘴豆在遗传上更接近野生种。比较分析预测了驯化过程中野生和栽培物种之间的基因流动。分子多样性和群体遗传结构的测定，使用15,096全基因组单核苷酸多态性揭示了一个混合驯化模式之间的栽培（德西和卡布里）和野生鹰嘴豆加入属于三个人口群体，反映显着的影响，父母或地理来源的品种特定的人口分类。本研究所获得的多态性序列资源将有助于鹰嘴豆的驯化研究和鹰嘴豆野生种质资源的定向利用。
Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea.