Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University Research and Development Park, Bundoora, VIC, 3083, Australia.
Theor Appl Genet. 2014 Mar;127(3):703-13. doi: 10.1007/s00122-013-2252-0. Epub 2013 Dec 27.
Large-scale SNP discovery and dense genetic mapping in a lentil intraspecific cross permitted identification of a single chromosomal region controlling tolerance to boron toxicity, an important breeding objective. Lentil (Lens culinaris Medik.) is a highly nutritious food legume crop that is cultivated world-wide. Until recently, lentil has been considered a genomic 'orphan' crop, limiting the feasibility of marker-assisted selection strategies in breeding programs. The present study reports on the identification of single-nucleotide polymorphisms (SNPs) from transcriptome sequencing data, utilisation of expressed sequence tag (EST)-derived simple sequence repeat (SSR) and SNP markers for construction of a gene-based genetic linkage map, and identification of markers in close linkage to major QTLs for tolerance to boron (B) toxicity. A total of 2,956 high-quality SNP markers were identified from a lentil EST database. Sub-sets of 546 SSRs and 768 SNPs were further used for genetic mapping of an intraspecific mapping population (Cassab × ILL2024) that exhibits segregation for B tolerance. Comparative analysis of the lentil linkage map with the sequenced genomes of Medicago truncatula Gaertn., soybean (Glycine max [L.] Merr.) and Lotus japonicus L. indicated blocks of conserved macrosynteny, as well as a number of rearrangements. A single genomic region was found to be associated with variation for B tolerance in lentil, based on evaluation performed over 2 years. Comparison of flanking markers to genome sequences of model species (M. truncatula, soybean and Arabidopsis thaliana) identified candidate genes that are functionally associated with B tolerance, and could potentially be used for diagnostic marker development in lentil.
大规模 SNP 发现和在扁豆种内杂交中的密集遗传作图允许鉴定单个控制硼毒性耐受性的染色体区域，这是一个重要的育种目标。扁豆（Lens culinaris Medik.）是一种营养丰富的食用豆类作物，在全球范围内种植。直到最近，扁豆一直被认为是基因组的“孤儿”作物，限制了标记辅助选择策略在育种计划中的可行性。本研究报告了从转录组测序数据中鉴定单核苷酸多态性（SNP），利用表达序列标签（EST）衍生的简单重复序列（SSR）和 SNP 标记构建基于基因的遗传连锁图谱，以及鉴定与硼（B）毒性耐受性主要 QTL 紧密连锁的标记。从扁豆 EST 数据库中鉴定出 2956 个高质量 SNP 标记。进一步从小集的 546 个 SSR 和 768 个 SNP 中选择用于种内作图群体（Cassab×ILL2024）的遗传作图，该群体表现出对 B 耐受性的分离。将扁豆连锁图谱与 Medicago truncatula Gaertn.、大豆（Glycine max [L.] Merr.）和 Lotus japonicus L.的测序基因组进行比较分析表明，存在着保守的宏同线性块，以及一些重排。基于两年的评估，发现一个单一的基因组区域与扁豆对 B 耐受性的变异有关。将侧翼标记与模式物种（M. truncatula、大豆和拟南芥）的基因组序列进行比较，鉴定出与 B 耐受性功能相关的候选基因，这些基因可能用于扁豆的诊断标记开发。
