Ruperao Pradeep, Gandham Prasad, Odeny Damaris A, Mayes Sean, Selvanayagam Sivasubramani, Thirunavukkarasu Nepolean, Das Roma R, Srikanda Manasa, Gandhi Harish, Habyarimana Ephrem, Manyasa Eric, Nebie Baloua, Deshpande Santosh P, Rathore Abhishek
Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, LA, United States.
Front Plant Sci. 2023 Mar 17;14:1143512. doi: 10.3389/fpls.2023.1143512. eCollection 2023.
Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A -based sorghum race sequence comparison identified the conserved s of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Co-localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed signatures will be useful in the future to identify the sorghum race and for trait and SNP markers for assisting in plant breeding programs.
由于进化差异，高粱品种群体表现出显著的遗传和形态变异。基于A的高粱品种序列比较确定了高粱所有272份种质的保守序列，特定品种的遗传特征确定了10321个基因（PAVs）中的基因变异性。为了了解高粱品种结构、多样性和驯化情况，在一组来自272份高粱种质的基因型数据中采用了基于深度学习的变异检测方法。这些数据产生了170万个高质量的全基因组单核苷酸多态性（SNP），并通过不同的（iHS和XP-EHH）统计方法进行全基因组扫描，确定了选择特征（包括正向和负向）区域。我们发现了2370个与选择特征相关的基因，包括分布在10条染色体上的179个选择清除区域。这些经历选择压力的区域与先前报道的数量性状位点（QTL）和基因的共定位表明，选择特征可能与生物量和株高等重要农艺性状的驯化有关。所开发的特征在未来将有助于鉴定高粱品种以及用于辅助植物育种计划的性状和SNP标记。
