Ruperao Pradeep, Thirunavukkarasu Nepolean, Gandham Prasad, Selvanayagam Sivasubramani, Govindaraj Mahalingam, Nebie Baloua, Manyasa Eric, Gupta Rajeev, Das Roma Rani, Odeny Damaris A, Gandhi Harish, Edwards David, Deshpande Santosh P, Rathore Abhishek
International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India.
Genomics and Molecular Breeding Lab, ICAR-Indian Institute of Millets Research, Hyderabad, India.
Front Plant Sci. 2021 Jun 1;12:666342. doi: 10.3389/fpls.2021.666342. eCollection 2021.
Sorghum ( L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.
高粱(L.)是干旱和雨养生产生态系统中的主要粮食作物。高粱在可持续农业中发挥着关键作用,被视为一种智能作物,有望克服发展中国家的粮食和营养不安全问题。高粱泛基因组的开发和表征将有助于深入了解基因组多样性和功能,从而推动高粱品种改良。我们利用参考基因组以及354份属于不同种族的遗传多样的高粱种质构建了高粱泛基因组。我们探索了泛基因组的结构和功能特征,并阐述了其在支持遗传增益方面的作用。新构建的泛基因组共有35719个基因,核心基因组有16821个基因,每个品种平均有32795个基因。可变基因富含环境响应基因,并根据高粱种质的种族进行分类。我们发现53%的基因存在缺失变异,其中一些可变基因预计与干旱适应性状在功能上相关。利用泛基因组中的200多万个单核苷酸多态性(SNP)进行关联分析,鉴定出398个与重要农艺性状显著相关的SNP,其中92个位于基因中。干旱基因表达分析鉴定出1788个与不同条件在功能上相关的基因,其中79个在参考基因组组装中不存在。本研究提供了高粱全面的基因组多样性资源,可用于基因组辅助作物改良。