基于巢式关联群体挖掘高蛋白大豆新种质HJ117蛋白含量QTL

Knowledge of protein QTL positions, effects and their effects on yield, is required for efficient soybean protein improvement by molecular breeding approach. The breeding line ‘HJ117’, with protein content of 52.99% has been developed from the cross of ‘Jidou 12’ × ‘ChaMoShiDou’. We have developed a nested association mapping (NAM) population by crossing a hub parents ‘HJ117’ with six soybean cultivars including one elite cultivar from USA, one high protein cultivar from Jilin province, and four elite cultivars from Huanghuaihai region. The NAM population consists of 1080 recombinant inbred lines (RILs) with 180 lines for each family. The parents had been sequenced with 10× sequence coverage and the progenies will be also sequenced by Genotyping-by-Sequencing (GBS). The high-density markers in the parents will be projected to the progenies for construction of the linkage map. The linkage analysis and association analysis will be used to identify the QTL underlying protein content, respectively. Meanwhile, the genetic effect of alleles from difference parents will be estimated and the allelism to the allele from HJ117 will also be evaluated. Based on the QTL mapping results, the QTL heterozygous lines will be selected from the family and be used to develop residual heterozygous lines (RHL) using markers for fine mapping. The tightly-linked or co-segregation markers will be identified via fine mapping and will be used to identify candidate gene underlying the QTL. In order to evaluate the genetic effect on yield of the protein QTL, the near isogenic lines (NIL) will be nursed from RHL. The resulting NAM population will be shared among the soybean research and breeding community. The resulting high protein content breeding lines and the related QTL information will help the soybean breeder to develop novel cultivars more efficiently.

明确高蛋白大豆种质中蛋白含量QTL的位置、效应和对产量的影响，是实现高蛋白分子设计育种的基础。本项目以蛋白含量达到52.99%的新种质HJ117为共同亲本，分别与国外引进骨干亲本、东北高蛋白品种和黄淮生态区主栽品种杂交，培育巢式关联群体。亲本重测序与后代简化基因组测序相结合，构建高密度遗传图谱。连锁分析与关联分析相结合，初步定位蛋白含量QTL，比较QTL在不同遗传背景下和不同等位变异间的效应差别。根据初步定位结果，筛选重组率高的组合，培育高蛋白主效QTL剩余杂合系群体，通过精细定位确定紧密连锁标记和候选基因。在剩余杂合系群体中培育主效QTL近等基因系，明确主效QTL对产量、脂肪含量的影响。通过本项目实施，将培育首个高蛋白大豆巢式关联群体；挖掘高蛋白新种质HJ117中的蛋白含量QTL，直接应用于我国高蛋白大豆育种。

明确高蛋白大豆种质中蛋白含量QTL的位置、效应和对产量的影响，是实现高蛋白分子设计育种的基础。本项目以蛋白含量达到52.99%的新种质HJ117为共同亲本，分别与国外引进骨干亲本Hobbit（蛋白含量38.8%）、东北高蛋白品种吉育101（蛋白含量48.1%）、黄淮海主栽品种中黄42（蛋白含量45.1%）、郑196（蛋白含量42.8%）、齐黄34（蛋白含量42.8%）和徐豆16（蛋白含量42.6%）杂交，培育获得包含1080个家系的巢式关联群体。利用HiFi测序数据并以Hi-C测序数据作为辅助，对HJ117的基因组进行从头组装，达到染色体水平。Contig总长为 1041.94 Mb，Contig N50长度达到19.32 Mb；Scaffold 总长1031.40 Mb，Scaffold N50 长度达到48.41Mbp。开发了基于目标位点测序（GBTS）检测大豆基因型的新技术，降低了本项目大规模基因型检测成本。绘制了Hobbit×HJ117、吉育101×HJ117、中黄42×HJ117、郑196×HJ117、齐黄34×HJ117和徐豆16×HJ117等6个组合的遗传图谱。并结合3年表型数据，在6个组合中，分别定位了10个、8个、52个、53个、7个和7个蛋白含量QTL。通过高精度连锁分析精细定位QTL，根据双亲全基因组重测序结果，筛选到30个候选基因，进一步筛选出在种子中高表达、且基因功能注释与蛋白质合成或碳氮代谢相关的候选基因7个。通过4个自然群体GWAS分析，确定了主效位点qPRO_15_1候选基因。通过基因编辑验证了候选基因Glyma.15g048700的功能。通过田间调查，分析了候选基因双突变体材料开花延迟、生育期延长、油份含量降低、百粒重降低且10株粒重降低。还通过代谢组学研究揭示HJ117及其近等基因系中与蛋白质/脂肪含量显著相关的代谢物。项目执行期间，发表本项目相关论文6篇，获得发明专利5项，培养在站博士后2名，毕业硕士生2名。通过本项目实施，培育出首个高蛋白大豆巢式关联群体；挖掘高蛋白新种质HJ117中的蛋白含量QTL，可直接应用于我国高蛋白大豆育种。