Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
Nat Commun. 2023 Jun 21;14(1):3694. doi: 10.1038/s41467-023-38915-6.
Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21 century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
指高粱是一种在东非、印度和尼泊尔广泛种植的主要粮食作物。长期以来，指高粱被认为是“穷人的庄稼”，但在过去十年中，由于其对气候变化的适应能力以及谷物的营养价值，它重新受到关注。为了将指高粱的育种带入 21 世纪，我们在这里展示了一个染色体级别的参考基因组的组装和注释。我们发现，这个约 130 万年的异源四倍体具有高度的同源基因保留，并且缺乏亚基因组优势。群体结构主要是由几个染色体的着丝粒区域中大量野生片段的差异存在驱动的。性状图谱分析，以及对候选基因变异的分析表明，花药和柱头的紫色丧失与玉米 R1/B1 和拟南芥 GL3/EGL3 类黄酮调节基因的指高粱同源基因的功能丧失突变有关。这些基因敲除不会影响种子中原花青素的产生。
