Detection and analysis of QTL for panicle length in rice using a high-density genetic map
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摘要:目的
深入挖掘与穗长相关的新基因,为水稻穗长调控的遗传机理研究及分子育种提供依据。
方法以2个优良亲本‘ZP37’和‘R8605’及其杂交衍生的208个高世代重组自交系(Recombinant inbred lines,RILs)为作图群体,利用全基因组重测序高密度连锁图谱对3个不同环境下的穗长数量性状座位(Quantitative trait locus,QTL)进行定位,同时分析它们的聚合效应。
结果共检测到11个穗长QTL,分别分布在第3、4、7、8、9和12号染色体上,其似然函数比对数值(Log of odds,LOD)介于3.07~12.87之间,贡献率在2.17%~10.94%之间,有7个QTL是新位点,其余4个QTL位点与已报道的穗长基因和QTL位置重叠或相近。在2个不同环境下重复检测到4个稳定的QTL位点;对聚合了不同数量穗长QTL株系的分析结果表明,穗长QTL表现出累加效应,QTL数量的增加能显著增加水稻穗长。
结论本研究结果为水稻穗长QTL的克隆和功能解析奠定坚实的基础,为水稻高产育种提供理论依据和遗传资源。
Abstract:ObjectiveTo deeply explore new genes related to panicle length and provide a basis for the study of genetic mechanism of panicle length regulation and molecular breeding in rice.
MethodTwo superior parents, ‘ZP37’ and ‘R8605’, as well as 208 recombinant inbred lines (RILs) derived from the cross of ZP37/R8605 were used as a mapping population to locate quantitative trait loci (QTLs) for panicle length in three different environments through the high-density linkage map of whole genome resequencing, and to analyze their pyramiding effects.
ResultA total of 11 QTLs for panicle length were detected on chromosomes 3, 4, 7, 8, 9 and 12, with the logs of odds (LODs) ranging from 3.07 to 12.87 and contribution rates ranging from 2.17% to 10.94%, seven of the QTLs were new loci, and the remaining four QTLs overlapped or were close to the reported panicle length genes and QTLs. Among them, four stable QTLs were detected repeatedly in two different environments, and by analyzing the lines that pyramiding different numbers of panicle length QTLs, the results showed that the panicle length QTLs showed an additive effect, and the increase in the number of QTLs significantly increased the panicle length of rice.
ConclusionThe results of this study provide a solid foundation for cloning and functional analysis of rice panicle length QTLs, as well as a theoretical basis and genetic resources for high-yield rice breeding.
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Keywords:
- Oryza sativa L. /
- Spike length /
- QTL mapping /
- High-density genetic map
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表 1 穗长在RIL群体中的分布情况
Table 1 Distribution of panicle length traits in RIL population
环境
Environment亲本穗长/cm
Parent panicle length重组自交系穗长
RIL panicle lengthZP37 R86051) 平均值/cm
Mean变幅/cm
Range偏度
Skewness峰度
Kurtosis变异系数/%
CV2019 23.10 37.56** 29.08 23.20~38.67 0.42 −0.13 0.11 2020 23.57 34.63** 26.50 19.87~37.20 0.50 1.04 0.11 2022 23.48 32.05** 26.29 20.86~33.80 0.29 0.18 0.08 1)“**”表示与‘ZP37’株系相比差异显著(P < 0.01,t 检验)
1) “**” indicates significant difference from ‘ZP37’ strains (P < 0.01, t test)表 2 不同环境下水稻穗长QTL 分析
Table 2 QTL analysis of panicle length under different environments
位点
QTL染色体
Chr.物理位置/bp
Physical position2019 2020 2022 LOD 加性效应
Additive
effect贡献率/%
PVELOD 加性效应
Additive
effect贡献率/%
PVELOD 加性效应
Additive
effect贡献率/%
PVEqPL3-1 3 6992384—7197429 3.11 −0.63 2.28 qPL3-2 3 7324223—7890278 3.43 −0.71 2.89 qPL4-1 4 20619799—20702562 6.22 −0.68 4.54 qPL4-2 4 24259618—24399641 3.81 −0.69 2.17 3.94 −0.68 2.66 qPL7-1 7 14356324—14982725 5.21 0.66 2.45 3.14 0.53 2.75 qPL7-2 7 17321645—17418744 3.12 0.53 2.77 qPL8-1 8 25112712—26010194 12.87 −1.39 10.94 6.33 −0.80 6.39 qPL8-2 8 27500184—27682717 5.99 −1.13 5.87 qPL9 9 20564403—20770874 3.22 −0.82 3.08 5.42 −0.70 4.88 qPL12-1 12 7167759—7401747 3.31 −0.94 4.02 qPL12-2 12 14722574—14918715 3.07 −0.77 2.70 表 3 穗长QTL的聚合效应分析1)
Table 3 Pyramiding effect of the QTLs for panicle length
株系类型 QTL RIL数量
No. of RILs不同年份穗长/cm Panicle length in different years qPL4-2 qPL8-1 qPL9 2019 2020 2022 Hap 1 + + + 24 32.57a 29.86a 28.75a Hap 2 − + + 18 29.48bc 27.15b 26.92bc Hap 3 + + − 17 30.39b 27.80b 27.23b Hap 4 + − + 34 29.63bc 26.81bc 26.91bc Hap 5 − + − 15 28.91bcd 26.34bcd 25.71cd Hap 6 − − + 30 28.47cde 25.61cde 25.62d Hap 7 + − − 37 27.89de 25.43de 25.57d Hap 8 − − − 20 26.91e 24.44e 24.19e 1) “+”和“−”分别表明含有和不含增效等位基因;同列数据后的不同小写字母表示相同环境下不同株系类型之间差异显著(P < 0.05, LSD法)
1) “+” and “−” indicate the presence and absence of favorable alleles respectively; Different lowercase letters of the same column indicate significant differences among different types of strains under the same environment (P < 0.05,LSD method) -
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