Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Plant Biol. 2020 Oct 15;20(1):474. doi: 10.1186/s12870-020-02567-1.
Goji (Lycium spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits.
In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F individuals derived from L. chinense and L. barbarum and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3495 SLAF markers on 12 LGs, spanning 1649.03 cM with 0.47 cM average interval. Female and male parents and F individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018-2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. Six Promising QTLs (qFW10-6.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1, qLA10-2.1) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32-71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness (qFS3-1, qFS5-2) and fruit firmness (qFF10-1) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular, qFL10-2.1 was co-located with qLL10-2.1, qLD10-2.1 and qLA10-2.1 among stable QTLs, harbored tightly linked markers, while qLL10-1 was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures.
This report highlights the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.
枸杞（Lycium spp.，2n = 24）是一种结果实的木本植物，因其具有广泛的药用和营养价值而被作为超级食品而广受欢迎。与果实大小相关的特性对于评估小果枸杞和植物结构非常重要。作物的驯化特性是在数量上调控的，但很少有研究尝试在与果实特性相对应的基因组区域进行研究。
本研究基于 305 个来自中华枸杞和宁夏枸杞的 F1 个体，利用特异区域扩增片段（SLAF）测序建立了高分辨率图谱，用于基于从头 SNP 检测的数量性状位点（QTL）分析。遗传图谱包含 3495 个 SLAF 标记，分布在 12 条 LG 上，总长 1649.03cM，平均间隔为 0.47cM。母本和父本以及 F1 个体的测序深度分别为 111.85 倍、168.72 倍和 35.80 倍。表型数据连续两年（2018-2019 年）采集，但在额外一年（1819 年）将两年的平均值数据合并。共检测到 117 个与多个性状相关的 QTL，其中 78 个在两年内，36 个在额外的一年。发现了 6 个有前途的 QTL（qFW10-6.1、qFL10-2.1、qLL10-2.1、qLD10-2.1、qLD12-4.1、qLA10-2.1），影响果实重量、果实长度和叶片相关属性，涵盖 LG10 上 27.32-71.59cM 的区间，峰值 LOD 为 10.48 和 14.6% PVE。还鉴定了 3 个针对果实甜度（qFS3-1、qFS5-2）和果实硬度（qFF10-1）的 QTL。值得注意的是，LG10 上的各种性状 QTL 存在重叠，特别是 qFL10-2.1 与 qLL10-2.1、qLD10-2.1 和 qLA10-2.1 共定位在稳定 QTL 中，紧密连锁的标记，而 qLL10-1 是一个具有 14.21 个最高 LOD 和 19.3%方差的主要 QTL。由于 LG10 含有重要的性状 QTL，我们可以推测它可能是调节果实大小和植物结构的热点区域。
本报告强调了使用 SLAF-seq 构建的极其饱和的连锁图谱以及对枸杞果实大小相关属性有贡献的新基因座。我们的研究结果将为枸杞的驯化特性提供启示，并进一步加强其分子和遗传基础；此外，这些发现将更好地促进参考基因组的组装，确定潜在的候选基因，并进行基于标记的辅助育种。
