Gebeyehu Adane, Hammenhag Cecilia, Tesfaye Kassahun, Vetukuri Ramesh R, Ortiz Rodomiro, Geleta Mulatu
Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden.
Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia.
Front Plant Sci. 2022 May 11;13:882136. doi: 10.3389/fpls.2022.882136. eCollection 2022.
Genomic resources and tools are essential for improving crops and conserving their genetic resources. (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed , resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium ( < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.
基因组资源和工具对于改良作物及其遗传资源的保护至关重要。诺格（Noug）是一种异花授粉的食用油籽作物，其基因组资源极为有限。因此，对30个诺格基因型进行了基于RNA测序的转录组测序，以生成新的基因组资源并评估其用途。这些基因型包括自交亲和型和自交不亲和型，它们在成熟时间、光周期敏感性或油含量及品质方面存在差异。在Illumina HiSeq 2500平台上进行RNA测序，并对转录本进行重构，共获得409,309个单基因。对这些单基因进行简单序列重复（SSR）特征分析，并作为单核苷酸多态性（SNP）检测的参考。在409,309个单基因中的35,639个中总共鉴定出40,776个SSR。其中，单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸和六核苷酸重复分别占55.4%、20.8%、21.1%、2.3%、0.2%和0.2%。单基因及其SSR的平均G+C含量分别为40%和22.1%。绝大多数单核苷酸重复SSR（97%）为A/T型。AG/CT和CCA/TGG是最常见的二核苷酸和三核苷酸重复SSR。在每个基因型中发现了不同数量的单核苷酸多态性（SNP）位点，其中1,687个在所有30个基因型中都有，5,531个在其中28个基因型中存在。5,531个SNP的平均观察杂合度为0.22；其中19.4%的多态性信息含量高于0.30，而17.2%显著偏离哈迪-温伯格平衡（<0.05）。在聚类分析和主坐标分析中，基因型被分为四个主要类群。就群体结构而言，这些基因型最好由三个遗传群体代表，每个群体内部都有显著的混合。由于遗传基础狭窄，自交亲和型基因型之间的遗传相似性高于自交不亲和型基因型之间的遗传相似性。发现具有早熟和高油含量等优良特性的基因型在遗传上具有多样性，因此可以通过杂交培育出具有多种优良性状的优良品种。本研究中开发的基因组资源对于推进诺格的研究至关重要，如遗传连锁图谱绘制和全基因组关联研究，这可能会引领基于基因组的育种。
