利用高密度遗传图谱定位水稻耐低氧萌发QTL

Mapping of QTLs for Tolerance of Hypoxia Germination in Rice with a High-density Genetic Map

【目的】耐低氧萌发能力是水稻直播适应性的核心性状之一。采用直播型温带粳稻品种Francis和多穗型优质恢复系R998衍生的重组自交系群体开展水稻耐低氧萌发QTL定位研究,旨在为直播稻品种培育提供新的有价值的基因资源,促进直播稻新品种培育和直播稻生产方式的推广。【方法】以28℃淹水10 cm暗培养7 d的水稻胚芽鞘长、芽长和最大根长作为耐低氧萌发能力指标,通过低倍基因组重测序构建含有3106个bin标记的高密度遗传图谱,采用WinQTL Cart 2.5进行QTL扫描。【结果】低氧萌发条件下,Francis的胚芽鞘长度和根长显著高于R998,但是两者芽长差异不显著。构建的遗传图谱总图距为3646.2 cM,其中12号染色体标记数最少,1号染色体标记数最多,分别为174个和389个。遗传图谱的标记平均图距为1.21 cM,各染色体的平均图距范围为0.68~1.84 cM,5 cM以上的Gap比例为0.36%。采用复合区间作图法(CIM),共检测到分布于5条染色体上的6个耐低氧萌发相关QTL。其中,控制胚芽鞘长度、芽长和根长的QTL个数分别为3、1、2个。表型贡献率超过10%的2个QTL是胚芽鞘长度位点qCL9和芽长位点qSL5,二者分别解释群体表型变异的13.39%和10.78%。qCL9与根长QTL qRL2-1的增效等位基因均来自亲本Francis,其余4个QTL的增效等位基因来自亲本R998。6个QTL中有3个暂未见报道,可能是新的QTL。【结论】Francis和R998低氧萌发特性存在显著差异,双亲中均含有耐低氧萌发的增效等位基因。qCL9和qSL5是分别影响胚芽鞘长和芽长的主效QTL,在直播稻分子育种中具有潜在应用价值。

【Objective】Tolerance to hypoxia germination is one of the key traits for direct-seeding adaptability of rice.The temperate direct-seeding japonica rice variety Francis and multi-panicle indica restorer line R998 were used for QTL mapping of hypoxia germination related traits,aiming to provide new valuable gene resources for developing direct-seeding rice varieties and the promotion of direct-seeding rice production methods.【Method】The coleoptile length,shoot length and maximum root length of rice seedlings submerged in 10-cm-depth water in the dark for 7 days at 28℃were recorded as indicators of hypoxia germination tolerance capacity.A high-density genetic map containing 3106 bin markers was constructed by low-coverage genome re-sequencing,and QTL scanning was performed with WinQTL Cart 2.5.【Result】Under the condition of hypoxia germination,the coleoptile length and root length of Francis are significantly higher than those of R998,but there is no significant difference in shoot length between them.The total genetic distance of the constructed genetic map is 3646.2 cM,in which the number of markers on chromosome 12 is the least,and that on chromosome 1 is the most,with 174 and 389,respectively.The average marker distance in the genetic map is 1.21 cM,the marker distance of each chromosomes is 0.68-1.84 cM,and the gaps above 5 cM account for 0.36%.By using composite interval mapping(CIM),six QTLs related to hypoxia germination tolerance are detected on 5 chromosomes.Among them,the number of QTLs controlling coleoptile length,shoot length and root length are 3,1 and 2,respectively.The coleoptile locus qCL9 and the shoot length locus qSL5 had a phenotypic variance explained(PVE)over 10%,which are 13.39%and 10.78%,respectively.The beneficial allele of qCL9 and the root length locus qRL2-1 come from the parent Francis,while the other four beneficial alleles are provided by the parent R998.Three of the six QTLs have not been reported previously,therefore,they may be novel QTLs.【Conclusion】In summary,there is significant difference between Francis and R998 in hypoxia germination,and both parents have beneficial alleles for hypoxia germination tolerance.qCL9 and qSL5 are major effect QTLs controlling hypoxia germination tolerance and have practical value in the molecular breeding of direct-seeding rice.