Table_2_Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars.xlsx

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

龙爪稷（Eleusine coracana (L.) Geartn.）是一种自花授粉双二倍体作物，以低投入栽培方式用于粮食与饲料生产，同时为小规模农户提供收入来源。为高效评估其遗传多样性以用于种质保存及育种项目，需开发并应用可表征其复杂四倍体基因组的多态性DNA标记。本研究基于公开可用的龙爪稷表达序列标签（expressed sequence tag, EST），开发了13个全新的表达序列标签衍生简单序列重复（expressed sequence tag-derived simple sequence repeat, EST-SSR）标记。本研究使用10个多态性简单序列重复（simple sequence repeat, SSR）标记（其中3个为基因组SSR，7个为全新EST衍生SSR），对产自埃塞俄比亚主产区的55份地方品种种质和5份栽培品种的龙爪稷遗传多样性进行了评估。共在10个基因座中检测到26个等位基因，每个基因座的平均观测等位基因数为5.6。各基因座的多态性信息含量（polymorphic information content, PIC）介于0.045（Elco-48）至0.71（UGEP-66）之间。不同种质间的遗传多样性水平差异较小，平均基因多样性估计值仅在0.44（种质216054）至0.68（种质237443）之间波动。同样，各区域州的遗传变异范围也较窄，介于0.54（奥罗米亚州）至0.59（阿姆哈拉州与提格雷州）之间。值得注意的是，地方品种种质的平均基因多样性（0.57）与栽培品种（0.58）相近。分子方差分析（analysis of molecular variance, AMOVA）结果显示，种质内部及种质间均存在显著的遗传变异。种质间的变异占总变异的18.8%（FST=0.19；P<0.001）。同样，地理区域间也存在显著遗传变异，占总变异的6.9%（P<0.001）。聚类分析、主坐标分析及群体结构分析结果表明，龙爪稷地方品种群体的遗传构成与其起源地理区域间相关性较弱，这一结果间接反映了地理区域内外群体间存在较强的基因流。本研究开发的全新EST-SSR标记可应用于多个研究方向，其中未表现多态性的标记可在更广泛的龙爪稷遗传资源中开展进一步测试。