通过全基因组关联分析发掘水稻磷高效利用相关位点及基因

Rice is the main food in our country. Modern rice breeding is now developing with disease resistant, stress tolerant, nutrient use efficient and highly productive green super rice cultivation. Phosphorite resources in China are serious shortage and the low phosphorus use efficiency of rice in season which causes environmental population and resource waste. So it is essential to discover the loci and genes associated with high phosphorus use efficiency from rice germplasm resources by the new technology and methods of the whole genome study. This project is based on the whole genome resequencing data of 304 kinds of rice germplasm showing high genetic diversity and acquisition of genotype data about 1.02 millions of single nucleotide polymorphisms (SNP). Phenotypic traits including tillers, plant height, leaf chlorophyll content, plant phosphate content and grain yields per plant are detected under three-level of phosphate supply in the fields over the years, and the physiological-biochemical traits of plant phosphate content, root secreting organic acid and the activity of root secreting acid phosphatase are investigated by nutritional cultivation under low-level and normal-level phosphate supply. Genome-wide association studies (GWAS) the physiological-biochemical characterization and phenotypic traits above, further developing local fine map of association and discovering the favorable alleles and haplotypes according to obviously associated sites and the information about the known phosphorus uptake and use genes. It has great application value to breeding rice lines with high phosphorus use efficient by combinations of rice varieties with high phosphorus use efficiency and high-yielding restorer lines and hybridization and backcrossing.

水稻是我国主要的粮食作物。培育优质高产抗病抗逆营养高效的绿色超级稻已成为现代水稻育种的重要方向，我国是磷矿资源严重不足的国家，且水稻磷肥当季利用率低，易造成环境污染和资源浪费。因此有必要利用水稻基因组研究的新技术和新方法，发掘水稻种质资源中磷高效相关位点及基因。本项目基于已完成304份遗传多样性高的水稻材料全基因组重测序并获得约102万个SNP位点的基因型数据。在三种磷水平处理下两年多重复田间试验中，测定水稻的分蘖数、株高、叶绿素含量、植株磷含量以及产量等表型特征；通过营养液培养在低磷和正常供磷条件下测定水稻植株磷含量、根系有机酸分泌量、酸性磷酸酶活性等生理生化特性。完成上述各性状的全基因组关联分析，针对显著关联位点和已知磷吸收利用相关基因等信息，开展局部的精细关联定位，发掘有利等位基因或者单元型。配制磷高效品种与高产恢复系等材料，杂交回交，培育具有育种应用价值的磷高效水稻品系。

水稻是我国主要的粮食作物。培育优质高产抗病抗逆营养高效的绿色超级稻已成为现代水稻育种的重要方向，我国是磷矿资源严重不足的国家，且水稻磷肥当季利用率低，易造成环境污染和资源浪费。本课题通过分析270份品种群体重测序数据，共计获得约300万SNP位点数据；根据270份自然群体品种生育期信息，除去生育期特别长或特别短的品种，最终选取200份品种在海南基地正常供磷水平和低磷条件下进行两个季节重复筛选与鉴定，重点考察株高、分蘖数、单株生物量、有效穗数和、单株产量等综合农艺性状，初步建立水稻磷高效筛选与评价指标。获得耐低磷水稻品种15个，将耐低磷品种与中心节水抗旱稻恢复系9299配置杂交组合，杂交后代在多年多点低磷条件下筛选与鉴定，获得耐低磷且节水抗旱新种质5份；通过全基因组关联分析技术进行田间和水培下表型性状和全基因组SNP位点的关联分析，在第1、3、4、7、8、9、10、11、12号染色体上检测到显著关联信号，进一步以相对单株生物量和产量为指标将群体材料分成耐低磷组和低磷敏感组进行耐低磷全基因组受选择染色体区域鉴定，发现第4、6、9、10和12号染色体上有耐低磷显著性选择区域，综合GWAS和全基因组受选择染色体区域；获得一批耐低磷和磷高效利用的显著关联SNP位点和7个候选基因，这些候选基因和分子标记可用于水稻磷高效遗传改良。