Studies of genetic diversity and genome-wide association for vitamin C content in lettuce (Lactuca sativa L.) using high-throughput SNP arrays.

IF 3.9 2区 生物学 Q1 GENETICS & HEREDITY
Plant Genome Pub Date : 2024-10-24 DOI:10.1002/tpg2.20518
Inés Medina-Lozano, Juan Ramón Bertolín, Jörg Plieske, Martin Ganal, Heike Gnad, Aurora Díaz
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Abstract

Lettuce (Lactuca sativa L.) is a source of beneficial compounds though they are generally present in low quantities. We used 40K Axiom and 9K Infinium SNP (single nucleotide polymorphism) arrays to (i) explore the genetic variability in 21 varieties and (ii) carry out genome-wide association studies (GWAS) of vitamin C content in21 varieties and a population of 205 plants from the richest variety in vitamin C ('Lechuga del Pirineo'). Structure and phylogenetic analyses showed that the group formed mainly by traditional varieties was the most diverse, whereas the red commercial varieties clustered together and very distinguishably apart from the rest. GWAS consistently detected, in a region of chromosome 2, several SNPs related to dehydroascorbic acid (a form of vitamin C) content using three different methods to assess population structure, subpopulation membership coefficients, multidimensional scaling, and principal component analysis. The latter detected the highest number of SNPs (17) and the most significantly associated, 12 of them showing a high linkage disequilibrium with the lead SNP. Among the 84 genes in the region, some have been reported to be related to vitamin C content or antioxidant status in other crops either directly, like those encoding long non-coding RNA, several F-box proteins, and a pectinesterase/pectinesterase inhibitor, or indirectly, like extensin-1-like protein and endoglucanase 2 genes. The involvement of other genes identified within the region in vitamin C levels needs to be further studied. Understanding the genetic control of such an important quality trait in lettuce becomes very relevant from a breeding perspective.

利用高通量 SNP 阵列研究莴苣(Lactuca sativa L.)中维生素 C 含量的遗传多样性和全基因组关联。
生菜(Lactuca sativa L.)是一种有益化合物的来源,但其含量通常较低。我们使用 40K Axiom 和 9K Infinium SNP(单核苷酸多态性)阵列:(i) 探索 21 个品种的遗传变异性;(ii) 对 21 个品种和维生素 C 含量最丰富的品种("Lechuga del Pirineo")的 205 株植物群体的维生素 C 含量进行全基因组关联研究(GWAS)。结构和系统进化分析表明,主要由传统品种组成的群体最具多样性,而红色商业品种聚集在一起,与其他品种有很大区别。利用三种不同的方法评估种群结构,即子种群成员系数、多维尺度和主成分分析,GWAS 在 2 号染色体的一个区域内持续检测到与脱氢抗坏血酸(维生素 C 的一种形式)含量有关的多个 SNP。主成分分析检测到的 SNP 数量最多(17 个),相关性也最显著,其中 12 个 SNP 与主 SNP 存在高度连锁不平衡。在该区域的 84 个基因中,有一些已被报道与其他作物的维生素 C 含量或抗氧化状态有关,有的是直接相关的,如编码长非编码 RNA、几个 F-box 蛋白和一个果胶酶/pectinesterase 抑制剂的基因,有的是间接相关的,如 extensin-1-like 蛋白和内切葡聚糖酶 2 基因。在该区域内发现的其他基因参与维生素 C 水平的情况还有待进一步研究。从育种的角度来看,了解莴苣如此重要的品质性状的遗传控制变得非常重要。
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来源期刊
Plant Genome
Plant Genome PLANT SCIENCES-GENETICS & HEREDITY
CiteScore
6.00
自引率
4.80%
发文量
93
审稿时长
>12 weeks
期刊介绍: The Plant Genome publishes original research investigating all aspects of plant genomics. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board gives preference to novel reports that use innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for agronomic improvement.
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