Department of Biological Sciences, University of Embu, Embu, Kenya.
Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
PLoS One. 2022 Sep 1;17(9):e0272955. doi: 10.1371/journal.pone.0272955. eCollection 2022.
Crotalaria is a plant genus that is found all over the world, with over 700 species of herbs and shrubs. The species are potential alternative food and industrial crops due to their adaptability to different environments. Currently, information on the genetic diversity and population structure of these species is scanty. Genotyping-by-sequencing (GBS) is a cost-effective high-throughput technique in diversity evaluation of plant species that have not been fully sequenced. In the current study, de novo GBS was used to characterize 80 Crotalaria accessions from five geographical regions in Kenya. A total of 9820 single nucleotide polymorphism (SNP) markers were obtained after thinning and filtering, which were then used for the analysis of genetic diversity and population structure in Crotalaria. The proportion of SNPs with a minor allele frequency (maf) > = 0.05 was 45.08%, while the Guanine-Cytosine (GC) content was 0.45, from an average sequence depth of 455,909 reads per base. The transition vs transversion ratio was 1.81 and Heterozygosity (He) ranged between 0.01-0.07 in all the sites and 0.04 to 0.52 in the segregating sites. The mean Tajima's D value for the population was -0.094, suggesting an excess of rare alleles. The fixation index (Fst) between the different populations based on the Wright Fst (1943) ranged from 0.0119 to 0.066 for the Eastern-Western and Nairobi-Western populations. Model based techniques of population structure analysis including structure, k-means and cross-entropy depicted eight clusters in the study accessions. Non-model based techniques especially DAPC depicted poor population stratification. Correspondence Analysis (CA), Principal coordinate analyses (PCoA) and phylogenetic analysis identified a moderate level of population stratification. Results from this study will help conservationists and breeders understand the genetic diversity of Crotalaria. The study also provides valuable information for genetic improvement of domesticated species.
鸡母珠是一种植物属，分布于世界各地，拥有超过 700 种草本和灌木。由于其对不同环境的适应性，这些物种是潜在的替代食物和工业作物。目前，有关这些物种的遗传多样性和种群结构的信息很少。基于测序的基因型分析（GBS）是一种经济高效的高通量技术，可用于评估尚未完全测序的植物物种的多样性。在本研究中，使用从头开始的 GBS 对来自肯尼亚五个地理区域的 80 个鸡母珠进行了基因分型。经过稀疏和过滤后，共获得了 9820 个单核苷酸多态性（SNP）标记，用于分析鸡母珠的遗传多样性和种群结构。具有次要等位基因频率（maf）>=0.05 的 SNP 比例为 45.08%，而鸟嘌呤-胞嘧啶（GC）含量为 0.45，平均序列深度为每个碱基 455909 个读取。转换与颠换比为 1.81，所有位点的杂合度（He）在 0.01-0.07 之间，分离位点的杂合度在 0.04 到 0.52 之间。基于 Wright Fst（1943）的不同群体之间的平均 Tajima's D 值为-0.094，表明存在过多的稀有等位基因。基于 Wright Fst（1943）的不同群体之间的固定指数（Fst）在东部-西部和内罗毕-西部群体之间的范围从 0.0119 到 0.066。基于模型的种群结构分析技术，包括结构、k-均值和交叉熵，在研究中的品系中描绘了 8 个聚类。非基于模型的技术，特别是 DAPC，描绘了较差的种群分层。对应分析（CA）、主坐标分析（PCoA）和系统发育分析确定了中等水平的种群分层。本研究的结果将帮助保护主义者和培育者了解鸡母珠的遗传多样性。该研究还为驯化物种的遗传改良提供了有价值的信息。
