Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA.
Bayer R&D Services LLC, Kansas City, MO 64153, USA.
J Adv Res. 2023 Jun;48:47-60. doi: 10.1016/j.jare.2022.08.020. Epub 2022 Sep 7.
The domestication bottleneck has reduced genetic diversity inwheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank.
The study aims to exploreGenotyping by sequencing (GBS) to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program.
TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie's and F-statistics (F index were used to determine the center of genetic diversity.
We found 65 % and 47 % duplicated accessions in Triticum timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and F scan uncovered a lower intra and higher inter-species differentiation. Distinct F regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1).Our results suggest that Israel, Jordan, Syria, and Lebanonas the hub of genetic diversity of wild emmer;Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for theT. timopheevii. Identified core set accessions preserved more than 93 % of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii.
The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.
驯化瓶颈减少了小麦的遗传多样性，因此有必要在育种计划中利用野生近缘种。野生四倍体小麦广泛应用于育种计划，但由于其形态特征，很难区分这些小麦，导致基因库中出现 accession 的错误分类/标记或重复。
本研究旨在利用测序基因型（GBS）对野生和驯化四倍体小麦进行鉴定，生成一组核心 accession，用于育种计划。
使用 TASSEL-GBS 流水线进行 SNP 发现，使用 fastStructure 确定群体结构，使用 PowerCore 生成核心集。使用 Nie 的核苷酸多样性矩阵和 F 统计量（F 指数）确定遗传多样性的中心。
我们发现 Triticum timopheevii 和 T. turgidum 中分别有 65%和 47%的 accession 是重复的。全基因组核苷酸多样性和 F 扫描揭示了较低的种内和较高的种间分化。在属于驯化基因的基因组区域中鉴定到了独特的 F 区：非脆茎（Btr1）和春化（VRN-1）。我们的结果表明，以色列、约旦、叙利亚和黎巴嫩是野生二粒小麦遗传多样性的中心；土耳其和格鲁吉亚是 T. durum 的中心；伊拉克、阿塞拜疆和亚美尼亚是 T. timopheevii 的中心。鉴定的核心集 accession 保存了超过 93%的可用遗传多样性。全基因组关联研究（GWAS）表明，T. timopheevii 对叶锈病的抗性可能与染色体片段有关。
本研究探索了 GBS 技术在数据减少的同时保持物种遗传多样性的潜力。野生种质显示出比驯化 accession 更高的分化，表明有足够的多样性可用于作物改良。核心集减少了复杂性，同时保留了基因库收集的遗传多样性，并有助于更稳健地对野生种质进行表征。
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