玉米基因组功能性InDel/PAV结构变异对苗期生物质相关性状杂种优势的遗传贡献

Maize (Zea mays L.) resequencing results have exhibited that the pervasive functional insert/deletion (InDel) and presence-absence variation (PAV), which reside in or proximity to a function gene, were scattered in the whole genome。However, the implications of functional InDel/PAV structural variation for heterosis remain unknown. Our previous studies have developed around 500 markers physically linked with the functional InDel/PAV variation by calling an effective depth of ⅹ50 coverage of B73 and Mo17 next generation sequencing datasets. Also some of these markers have been mapping on 10 maize linkages with the intermated B73 x Mo17 (IBM) recombinant inbred line (RIL) population. Here, we propose a serial genetic experiments to elucidate the potential roles of functional InDel/PAV in maize seedling heterosis using the triple testcross(TTC) design and a IBM population of 200 RILs crossed with both parents (B73 and Mo17)and their F1, respectively. The four biomass-related traits of these three populations at seedling stage of 21 days after planting(DAP) will be measured in three locations for two years, which include length of 3th leaf fully expanded(LFE), width of 3th LFE, area of 3th LFE and total aerial dry weight. The functional InDel/PAV responsible for heterosis of biomass-related traits will be identified using quantitative trait loci (QTL) detection methods. Subsequently, the genes resided in or proximity to the significant QTL will be under further investigation. The genetic relationships between the functional InDel/PAV variation and seedling heterosis will be established in this proposal, and the results are expected to have a positive impact on heterosis breeding efforts.

尽管玉米基因组中存在较多与基因紧密连锁的插入/缺失（InDel）及大片段有无变异（PAV）区域，但是这些功能性结构变异区对杂种优势的作用尚不明确。本项目拟通过全新的三重测交（TTC）交配设计对200株较高遗传分辨率intermated B73 x Mo17（IBM）重组自交系构建其与亲本B73、Mo17及F1杂交的三个测交群体，利用已发展的500个功能性InDel/PAV区域分子标记，结合播种后第21天苗期生物质相关性状（第三片展开叶的叶长、叶宽、叶面积及地上部分干物质重）两年三点的表型数据对目标性状杂种优势位点进行数量性状位点（QTL）定位，明确生物质相关性状杂种优势的主效位点，分析生物质相关性状杂种优势的遗传效应，探索功能性InDel/PAV结构变异与杂种优势的关系，以期从基因组结构变异角度为杂种优势遗传机理的阐明提供新补充。

玉米基因组中存在较多插入/缺失（insertion/deletion, InDel）及大片段有无变异（presence/absence variation, PAV）区域，但是这些结构变异区对杂种优势的作用尚不明确。本项目利用B73参考基因组（V3）及Mo17基因组测序数据分析基因组结构变异，并通过三重测交交配设计对120株IBM（intermated B73 × Mo17）重组自交系构建其与亲本B73、Mo17及F1杂交的三个测交群体（TC(B), TC(M)和TC(F)），结合播种后第21天苗期生物质相关性状（叶长、叶宽、叶面积及地上部分干重）的表型数据对目标性状杂种优势位点进行数量性状位点（quantitative trait loci, QTL）分析。. 经过Mo17基因组组装序列与B73参考基因组的比对，共获得119个PAV，其中57个得到PCR验证并通过IBM分离群体整合到遗传连锁图谱上。Blastx分析发现，15.8% PAV基因与抗病性有关，该结果表明基因组PAV对玉米的抗病性起重要作用。. 生物质相关性状的杂种优势通过中亲优势评价。植株干重中亲优势最强（139.2%），叶面积呈中度优势 (40.6%)，叶长和叶宽的中亲优势较弱（分别为19.7% 和18.3%）。群体性状分析发现，TC(M)群体的叶宽及叶面积性状值显著高于TC(B)，植株干重性状值显著低于TC(B)。这与Mo17与B73生物质性状值相一致，表明叶宽及叶面积的有利等位基因来自Mo17而植株干重性状的有利等位基因来自B73。相关性分析表明所有生物质相关性状间具有显著的相关关系但相关系数不同。叶宽与叶面积间具有最强的相关性，相关系数高达0.833。. 本研究共得到13个生物质相关性状QTL，包括8个加性，3个显性和2个加显上位性QTL。单个QTL位点的表型贡献率从7.9%到21.5%不等。对上位性互作QTL进一步剖分发现，叶长和叶宽分别检测到1对加加两位点互作，单位点表型贡献率基本相同，约为17%；叶长检测到2对显显两位点互作，总体可解释57.1%的表型变异。所有的两位点互作区段均没有定位到主效QTL。主效及互作QTL的鉴定结果表明生物质相关性状的杂种优势遗传基础较为复杂，该研究有助于加强对生物质相关性状杂种优势的理解。