骨干亲本蜀恢527的全基因组扫描以及产量相关性状的QTL
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摘要
蜀恢527因其一般配合力高、所配组合杂种优势强、衍生恢复系多等优点,被认为是现阶段杂交水稻育种的骨干亲本之一。本研究通过亲本性状遗传规律分析,结合全基因组扫描和QTL定位,阐明蜀恢527的遗传组成,确定其产量相关性状的关键基因组区域。研究结果如下：
1.系谱产量相关性状的分析并结合全基因组扫描,阐明蜀恢527关键基因组区域。
(1)系谱产量相关性状分析结果显示,结实率高低,每穗实粒数、每穗总粒数和有效穗的多少可能源自IR24-蜀恢527的遗传途径；而千粒重、单株重量的高低和有效穗的多少则可能源自圭630-R1318-蜀恢527的遗传途径。
(2)采用1050个SSR引物对骨干亲本及其亲本进行全基因组扫描,构建了蜀恢527基因组来源图谱。分析发现,所有品种共有(无多态性标记)的区段占62.94%；约有17.53%的区段可能来源于多个亲本(多态性标记不足以区分各亲本)；在蜀恢527形成过程中,R1318贡献了13.68%区段,辐36-2贡献了0.53%的区段,IR24贡献了1.32%的区段；同时,蜀恢527基因组内包含了4%的自身特有区段。
(3)根据系谱产量相关性状遗传途径和基因组来源图谱,初步确定了蜀恢527产量相关关键基因组区域。我们认为由蜀恢527的特有区段、IR24-蜀恢527遗传的区段和圭630-R1318-蜀恢527遗传的区段为蜀恢527的关键基因组区域。
2.以G46B×蜀恢527的F2群体为作图群体,对产量相关性状的QTLs进行了分析,以揭示蜀恢527产量相关性状的QTLs及其效应。
(1)选择覆盖水稻基因组的1895对微卫星引物进行筛选,其中244对SSR引物在母本G46B和父本蜀恢527之间表现出多态性,引物多态性频率为12.88%。
(2)用Mapmaker/EXP3.0软件构建了一张包含102个分子标记、覆盖水稻基因组2256.2cM、平均标记间遗传距离为22.12cM的遗传图谱。标记所覆盖的基因组最长的是第二染色体的两个连锁群(550.3cM),最短的是第11染色体(57.9cM)。标记间平均距离最长的是第8染色体(34.1cM),平均距离最短的是第11染色体(14.48cM)。本试验中所作出的遗传图谱标记顺序与已发表的图谱具有较好的一致性。
(3)对千粒重、每穗实粒数、每穗总粒数、结实率、有效穗和单株重量6个性状进行QTL分析,共检测到17个QTLs位点,分布于水稻第1、2、4、5、7、8号染色体上,可以解释部分的遗传变异。这些QTLs位点的遗传效应值介于3.02%～20.73%之间,其中效应值大于10%的位点有5个,效应值小于5%的QTL也检测到3个位点。17个QTLs研究的结果如下：
①检测到3个控制千粒重的QTLs,分别为qKGW-2-1.qKGW-2-2和qKGW-8-1。qKGW-2-1和qKGW-2-2位于第2号染色体标记RM3316-RM3774和RM3680-RM6853区间内,分别可解释6.99%和5.17%的表型变异率,qKGW-8-1位于第8号染色体RMl019-RM6925区间内,可解释7.88%的表型变异率。这3个控制千粒重的QTLs总贡献率为20.2％。qKGW-2-1和qKGW-8-1的加性效应方向相同,来自于蜀恢527,而qKGW-2-2的加性效应与它们相反,来自于G46B.qKGW-2-1和qKGW-8-1的显性效应方向相同,来自于G46B,而qKGW-2-2的显性效应与它们相反,来自父本蜀恢527。
②检测到3个控制实粒数的QTLs,分别为qFGP-1-1、qFGP-2-1和qFGP-4-1。qFG-1-1位于第1号染色体标记RM1003-RM8084区间内,可解释9.30%的表型变异率。qFGP-2-1位于第2号染色体RM3692-RM208区间内,可解释16.58%的表型变异率。qFGP-4-1位于第4号染色体RM8213-RM3658区间内,可解释4.28%的表型变异率。这3个控制实粒数的QTLs.总贡献率为30.16%。qFGP-2-1和qFGP-4-1的加性效应方向相同,来自于蜀恢527,而qFGP-1-1的加性效应与它们相反,来自于G46B。qFGP-1-1和qFGP-2-1的显性效应方向相同,来自于G46B,而qFGP-4-1的显性效应与它们相反,来自父本蜀恢527。
③检测到2个控制总粒数的QTLs,分别为qGPP-2-1和qGPP-4-1。qGPP-2-1位于第2号染色体标记RM3316-RM3774区间内,可解释7.11%的表型变异率。GGPP-4-1位于第4号染色体RM7051-RM7187区间内,可解释3.02%的表型变异率。这2个控制总粒数的QTLs总贡献率为10.13%。qGPP-2-1的加性效应与qGPP-4-1相反,来自于蜀恢527。而qGPP-2-1和qGPP-4-1的显性效应均来自母本G46B。
④检测到5个控制结实率的QTLs,分别为qSS-1-1、qSS-2-1、qSS-7-1、qSS-7-2和qSS-8-1。qSS-1-1位于第1号染色体标记RM5718-RM5919区间内,可解释8.69%的表型变异率。qSS-2-1位于第2号染色体标记RM3692-RM208区间内,可解释11.72%的表型变异率。qSS-7-1位于第7号染色体标记RM3831～M5344区间内,可解释7.92%的表型变异率。qSS-7-2位于第7号染色体标记RM3635～M7110区间内,可解释12.49%的表型变异率。qSS-8-1位于第8号染色体标记RM7057～M6010区间内,可解释3.04%的表型变异率。这5个控制结实率的QTLs总贡献率为43.86%。qSS-1-1、qSS-2-1和qSS-7-1的加性效应方向相同,均来自于蜀恢527,而qSS-7-2和qSS-8-1的加性效应与它们相反,来自于G46B。SS-7-2的显性效应来自父本G46B,其他四个的显性效应与它相反。
⑤检测到2个控制有效穗的QTLs,分别为qPN-5-1和qPN-8-1。qPN-5-1位于第5号染色体标记RM7653～M3663区间内,可解释5.16%的表型变异率。qPN-8-1位于第8号染色体RM4955～M7057区间内,可解释20.73%的表型变异率。这2个控制有效穗的QTLs总贡献率为25.89%。qPN-5-1与qPN-8-1的加性效应方向相同,均来自于G46B, qPN-5-1和qPN-8-1的显性效应方向也相同,均来自于G46B。
⑥检测到2个控制单株重量的QTLs,分别为qGYD-2-1和qGYD-8-1。qGYD-2-1位于第2号染色体标记RM3355～M6318区间内,可解释5.34%的表型变异率。qGYD-8-1位于第8号染色体RM4955～RM7057区间内,可解释10.58%的表型变异率。这2个控制单株重量的QTLs总贡献率为15.92%。qGYD-2-1与qGYD-8-1的加性效应方向相反,来自于蜀恢527,qGYD-2-1和qGYD-8-1的显性效应方向相同,均来自于G46B。
(4)该F2群体中也发现有15个偏分离分子标记,占总标记数的11.5%。其中,RM5586、M6554和RM8121三个标记偏G46B基因型,RM594、RM1092、RM5665、RM3308、RM20285和RM336偏蜀恢527基因型,在RM6717、RM1339和RM1364位点父母本纯合基因型偏高,杂合基因型偏低,而RM8240和RM1384位点父母本纯合基因型偏低,杂合基因型偏高,RM3572位点偏向G46B和杂合基因型。
3蜀恢527形成的核心关键区段产量相关性状候选QTLs
根据定位的QTLs及其效应,结合蜀恢527性状遗传途径和关键基因组区域分析,我们认为千粒重qKGW-2-1、qKGW-2-2、qKGW-8-1基因,单株重量qGYD-2-1基因,实粒数qFGP-2-1、qFGP-4-1基因,总粒数qGPP-2-1基因,结实率qSS-1-1、qSS-2-1、qSS-7-1、qSS-8-1基因可能是构成蜀恢527产量相关性状的关键基因。同时,整合文献报道产量相关性状的QTLs定位结果,也发现了一些可能解释关键区段影响产量相关性状的候选QTLs位点。
As one of the backbone parents currently used in hybrid rice breeding Shuhui 527 has many merits, such as high general combining ability, strong heterosis of hybrid combination, and many derivative R-lines. In order to clarify the genetic composition and the key genome regions of yield related characters of Shuhui 527, genomic scanning and QTLs analysis of Shuhui 527 were performed in this study. Main results were as the following:
1. The genetic composition and the key genome regions of yield related characters of Shuhui 527 were defined by genomic scanning and hereditas analysis of yield related traits.
(1). The results showed that seed-setting rate, filled grain number per panicle, grain number per panicle and panicles were possibly derived from the pedigree of IR24-Shuhui527; the weight of a thousand seeds, plant weight and panicles were possibly derived from the pedigree of Gui630-R1318-Shuhui 527.
(2).The genetic originated map of Shuhui 527 and its related ancestral parents were constructed by genomic scanning of materials in the pedigree with 1050 SSR primers. The results revealed that①the shared fragments of all varieties (i.e. none polymorphic fragments) accounted for 62.94%;②putative multi-originated fragments (polymorphic marker was unable to identify its origin) accounted for approximately 17.53%;③in the breeding process of Shuhui 527, R1318 had contributed 13.68% fragments, Fu36-2 had contributed 0.53% fragments, and IR24 had contributed 1.32% fragments;④Shuhui 527 had contributed 4% itself fragments.
(3). The key genome regions of Shuhui 527 was initially determined by the results of genomic scanning and hereditas analysis of yield related traits. Yield related key genormic regions of Shuhui527 were involved of those regions called Shuhui527 specific fragments, IR24 Originated fragments and R1318 originated fragments.
2. Using 288 G46B×Shuhui527 F2 descendants as mapping population, we constructed a rice SSR linkage map. By means of SSR linkage map, quantitative trait loci (QTLs) with 6 yield related traits including 1000-grain weight, Filled grain number per panicle, Grain number per panicle, seed setting rate, Pancile number, and Weight per plant were positioned and analyzed. Main results were as the following:
(1).244 SSR markers coming from 1895 SSR markers overlaying the rice genome had expressed polymorphism in both G46B and Shuhui527, polymorphism frequency was 12.88%.
(2).We constructed a molecular genetic map included 102 pairs of SSR markers which covered 2256.2 cM of rice genome, and the average distance between two markers spanned 22.12 cM with the population of G46BXShuhui527 F2. Two linkage groups of the chromosome 2 covered the longest (550.3cM) genome region, and the the linkage group of the chromosome 11 is the shortest (57.9 cM). The longest average distance between two markers spanned 34.1 cM and the shortest average distance between two markers spanned 14.48 cM, respectively. The linkage relationship of the markers was almost identical to previous studies.
(3). A total of 17 yield related QTLs were detected on chromosome 1,2, 4,5,7,8, respectively. Variation percentage explained by individual QTL ranged from 3.02% to 20.73%, out of which 5 QTLs explained more than 10% phenotypic variation and 3 QTLs explained less than 5% phenotypic variation. The detailed informations of 17 QTLs were as the following:
①Three QTLs were detected for 1000-grain weight, named qKGW-2-1, KGW-2-2 and qKGW-8-1. Totally, they explained 20.2% of the phenotypic variation. Among them, the qKGW-2-1 and qKGW-2-2 in the marker interval RM3316～RM3774 and RM3680～RM6853 of chromosome 2,accounting for 6.99% and 5.17% variation, respectively, the qKGW-8-1 were located in the marker interval RM1019-RM6925 of chromosome 8, accounting for 7.88% variation. The additive effects of qKGW-2-1 and qKGW-8-1 came from the male parent Shuhui527, however qKGW-2-2 came from the female parent G46B. The dominant effects of qKGW-2-1 and qKGW-8-1came from thefemale parent G46B, however qKGW-2-2 came from the male parent Shuhui527。
②Three QTLs were detected for filled grain number, named qFGP-1-1, qFGP-2-1, and qFGP-4-1. Totally, they explained 30.16% of the phenotypic variation. Among them, the qFGP-1-1 in the marker interval RM1003-RM8084 of chromosome 1, accounting for 9.30% variation, the qFGP-2-1 were located in the marker interval RM3692～RM208 of chromosome 2, accounting for 16.58% variation. the qFGP-4-1 in the marker interval RM8213～RM3658 of chromosome 4, accounting for 4.28% variation. The additive effects of qFGP-2-1 and qFGP-4-1 came from the male parent Shuhui527, however qFGP-1-1 came from the female parent G46B. The dominant effects of qFGP-1-land qFGP-2-1came from the female parent G46B, however qFGP-4-1came from the male parent Shuhui527。
③Two QTLs were detected for grain per panicle, named qGPP-2-land qGPP-4-1. Totally, they explained 10.13% of the phenotypic variation. Among them, the qGPP-2-1 in the marker interval RM3316-RM3774 of chromosome 2, accounting for 7.11% variation, the qGPP-4-1 were located in the marker interval RM7051～RM7187 of chromosome 4, accounting for 3.02% variation. The additive effects of qGPP-2-1 came from the male parent Shuhui527, however qGPP-4-1 came from the female parent G46B. The dominant effects of qGPP-2-land qGPP-4-1 came from thefemale parent G46B。
④Five QTLs were detected for seed setting rate, named qSS-1-1, qSS-2-1, qSS-7-1, qSS-7-2 and qSS-8-1. Totally, they explained 43.86% of the phenotypic variation. Among them, the qSS-1-1 in the marker interval RM5718- RM5919 of chromosome 1, accounting for 8.69% variation, the qSS-2-1 were located in the marker interval RM3692-RM208 of chromosome 2, accounting for 11.72% variation, the qSS-7-1 in the marker interval RM3831～RM5344 of chromosome 7, accounting for 7.92% variation. the qSS-7-2 were located in the marker interval RM3635～RM7110 of chromosome 7, accounting for 12.49% variation. the qSSS-1 were located in the marker interval RM7057-RM6010 of chromosome 8, accounting for 3.04% variation. The additive effects of qSS-1-1、qSS-2-land qSS-7-1 came from the male parent Shuhui527, however qSS-7-2 and qSSS-1 came from the female parent G46B. The dominant effects of qSS-7-2 came from the female parent G46B, however qSS-1-1 qSS-2-1、qSS-7-1 and qSS-8-1 came from the male parent Shuhui527。
⑤Two QTLs were detected for panicle number, named qPN-5-1 and qPN-8-1. Totally, they explained 25.89% of the phenotypic variation. Among them, the qPN-5-1 in the marker interval RM7653～RM3663 of chromosome 5, accounting for 5.16% variation, the qPN-8-1 were located in the marker interval RM4955-RM7057 of chromosome 8, accounting for 20.73% variation. The additive effects of qPN-5-land qPN-8-1 came from the female parent G46B. The dominant effects of qPN-5-land qPN-8-1 came from the female parent G46B.
⑥Two QTLs were detected for yield per plant, named qGYD-2-1 and qGYD-8-1. Totally, they explained 15.92% of the phenotypic variation. Among them, the qGYD-2-1 in the marker interval RM3355-RM6318 of chromosome 2, accounting for 5.34% variation, the qGYD-8-1 were located in the marker interval RM4955-RM7057 of chromosome 8, accounting for 10.58% variation. The additive effects of qGYD-2-1 came from the male parent Shuhui527, however qGYD-8-1 came from the female parent G46B. The dominant effects of qGYD-2-land qGYD-8-1 came from the female parent G46B.
(4) 288 F2 individuals derived from G46B and Shuhui527 were used to construct a genetic linkage map. Among the 131 markers,15 SSR markers, occupying 11.5% of the difference SSR markers showed genetic segregation distortion(P<0.05). RM5586, RM6554 and RM8121 inclined to the genotype of G46B;RM594、RM1092、RM5665、RM3308、RM20285 and RM336 inclined to the genotype of Shuhui527; RM6717, RM1339 and RM1364 inclined to the genotype of both G46B and Shuhui527,less heterozygous genotype;RM8240 and RM1384 inclined to the heterozygous genotype, less isozygoty genotype;RM3572 inclined to the genotype of both G46B and heterozygous genotype.
3 Candidate yield related QTLs in key fragments of Shuhui 527
The candidate QTLs of Shuhui 527 was initially determined by comparing the results of the key genomic fragments and the QTL locations and effects. Comparation suggested that qKGW-2-1、qKGW-2-2 and qKGW-8-1 for 1000-grain weight, qGYD-2-1 for weight per plant, qFGP-2-1 and qFGP-4-1 for filled grain number, qGPP-2-1 for grain per panicle, qSS-1-1、qSS-2-1、qSS-7-1 and qSS-8-1 for seed setting rate were candidate QTLs for the yield related traits of Shuhui 527.Besides, some other potential candidate QTLs were also discussed by integrating their genomic locations reported previously to the key genomic fragments of Shuhui 527.
1.系谱产量相关性状的分析并结合全基因组扫描,阐明蜀恢527关键基因组区域。
(1)系谱产量相关性状分析结果显示,结实率高低,每穗实粒数、每穗总粒数和有效穗的多少可能源自IR24-蜀恢527的遗传途径；而千粒重、单株重量的高低和有效穗的多少则可能源自圭630-R1318-蜀恢527的遗传途径。
(2)采用1050个SSR引物对骨干亲本及其亲本进行全基因组扫描,构建了蜀恢527基因组来源图谱。分析发现,所有品种共有(无多态性标记)的区段占62.94%；约有17.53%的区段可能来源于多个亲本(多态性标记不足以区分各亲本)；在蜀恢527形成过程中,R1318贡献了13.68%区段,辐36-2贡献了0.53%的区段,IR24贡献了1.32%的区段；同时,蜀恢527基因组内包含了4%的自身特有区段。
(3)根据系谱产量相关性状遗传途径和基因组来源图谱,初步确定了蜀恢527产量相关关键基因组区域。我们认为由蜀恢527的特有区段、IR24-蜀恢527遗传的区段和圭630-R1318-蜀恢527遗传的区段为蜀恢527的关键基因组区域。
2.以G46B×蜀恢527的F2群体为作图群体,对产量相关性状的QTLs进行了分析,以揭示蜀恢527产量相关性状的QTLs及其效应。
(1)选择覆盖水稻基因组的1895对微卫星引物进行筛选,其中244对SSR引物在母本G46B和父本蜀恢527之间表现出多态性,引物多态性频率为12.88%。
(2)用Mapmaker/EXP3.0软件构建了一张包含102个分子标记、覆盖水稻基因组2256.2cM、平均标记间遗传距离为22.12cM的遗传图谱。标记所覆盖的基因组最长的是第二染色体的两个连锁群(550.3cM),最短的是第11染色体(57.9cM)。标记间平均距离最长的是第8染色体(34.1cM),平均距离最短的是第11染色体(14.48cM)。本试验中所作出的遗传图谱标记顺序与已发表的图谱具有较好的一致性。
(3)对千粒重、每穗实粒数、每穗总粒数、结实率、有效穗和单株重量6个性状进行QTL分析,共检测到17个QTLs位点,分布于水稻第1、2、4、5、7、8号染色体上,可以解释部分的遗传变异。这些QTLs位点的遗传效应值介于3.02%～20.73%之间,其中效应值大于10%的位点有5个,效应值小于5%的QTL也检测到3个位点。17个QTLs研究的结果如下：
①检测到3个控制千粒重的QTLs,分别为qKGW-2-1.qKGW-2-2和qKGW-8-1。qKGW-2-1和qKGW-2-2位于第2号染色体标记RM3316-RM3774和RM3680-RM6853区间内,分别可解释6.99%和5.17%的表型变异率,qKGW-8-1位于第8号染色体RMl019-RM6925区间内,可解释7.88%的表型变异率。这3个控制千粒重的QTLs总贡献率为20.2％。qKGW-2-1和qKGW-8-1的加性效应方向相同,来自于蜀恢527,而qKGW-2-2的加性效应与它们相反,来自于G46B.qKGW-2-1和qKGW-8-1的显性效应方向相同,来自于G46B,而qKGW-2-2的显性效应与它们相反,来自父本蜀恢527。
②检测到3个控制实粒数的QTLs,分别为qFGP-1-1、qFGP-2-1和qFGP-4-1。qFG-1-1位于第1号染色体标记RM1003-RM8084区间内,可解释9.30%的表型变异率。qFGP-2-1位于第2号染色体RM3692-RM208区间内,可解释16.58%的表型变异率。qFGP-4-1位于第4号染色体RM8213-RM3658区间内,可解释4.28%的表型变异率。这3个控制实粒数的QTLs.总贡献率为30.16%。qFGP-2-1和qFGP-4-1的加性效应方向相同,来自于蜀恢527,而qFGP-1-1的加性效应与它们相反,来自于G46B。qFGP-1-1和qFGP-2-1的显性效应方向相同,来自于G46B,而qFGP-4-1的显性效应与它们相反,来自父本蜀恢527。
③检测到2个控制总粒数的QTLs,分别为qGPP-2-1和qGPP-4-1。qGPP-2-1位于第2号染色体标记RM3316-RM3774区间内,可解释7.11%的表型变异率。GGPP-4-1位于第4号染色体RM7051-RM7187区间内,可解释3.02%的表型变异率。这2个控制总粒数的QTLs总贡献率为10.13%。qGPP-2-1的加性效应与qGPP-4-1相反,来自于蜀恢527。而qGPP-2-1和qGPP-4-1的显性效应均来自母本G46B。
④检测到5个控制结实率的QTLs,分别为qSS-1-1、qSS-2-1、qSS-7-1、qSS-7-2和qSS-8-1。qSS-1-1位于第1号染色体标记RM5718-RM5919区间内,可解释8.69%的表型变异率。qSS-2-1位于第2号染色体标记RM3692-RM208区间内,可解释11.72%的表型变异率。qSS-7-1位于第7号染色体标记RM3831～M5344区间内,可解释7.92%的表型变异率。qSS-7-2位于第7号染色体标记RM3635～M7110区间内,可解释12.49%的表型变异率。qSS-8-1位于第8号染色体标记RM7057～M6010区间内,可解释3.04%的表型变异率。这5个控制结实率的QTLs总贡献率为43.86%。qSS-1-1、qSS-2-1和qSS-7-1的加性效应方向相同,均来自于蜀恢527,而qSS-7-2和qSS-8-1的加性效应与它们相反,来自于G46B。SS-7-2的显性效应来自父本G46B,其他四个的显性效应与它相反。
⑤检测到2个控制有效穗的QTLs,分别为qPN-5-1和qPN-8-1。qPN-5-1位于第5号染色体标记RM7653～M3663区间内,可解释5.16%的表型变异率。qPN-8-1位于第8号染色体RM4955～M7057区间内,可解释20.73%的表型变异率。这2个控制有效穗的QTLs总贡献率为25.89%。qPN-5-1与qPN-8-1的加性效应方向相同,均来自于G46B, qPN-5-1和qPN-8-1的显性效应方向也相同,均来自于G46B。
⑥检测到2个控制单株重量的QTLs,分别为qGYD-2-1和qGYD-8-1。qGYD-2-1位于第2号染色体标记RM3355～M6318区间内,可解释5.34%的表型变异率。qGYD-8-1位于第8号染色体RM4955～RM7057区间内,可解释10.58%的表型变异率。这2个控制单株重量的QTLs总贡献率为15.92%。qGYD-2-1与qGYD-8-1的加性效应方向相反,来自于蜀恢527,qGYD-2-1和qGYD-8-1的显性效应方向相同,均来自于G46B。
(4)该F2群体中也发现有15个偏分离分子标记,占总标记数的11.5%。其中,RM5586、M6554和RM8121三个标记偏G46B基因型,RM594、RM1092、RM5665、RM3308、RM20285和RM336偏蜀恢527基因型,在RM6717、RM1339和RM1364位点父母本纯合基因型偏高,杂合基因型偏低,而RM8240和RM1384位点父母本纯合基因型偏低,杂合基因型偏高,RM3572位点偏向G46B和杂合基因型。
3蜀恢527形成的核心关键区段产量相关性状候选QTLs
根据定位的QTLs及其效应,结合蜀恢527性状遗传途径和关键基因组区域分析,我们认为千粒重qKGW-2-1、qKGW-2-2、qKGW-8-1基因,单株重量qGYD-2-1基因,实粒数qFGP-2-1、qFGP-4-1基因,总粒数qGPP-2-1基因,结实率qSS-1-1、qSS-2-1、qSS-7-1、qSS-8-1基因可能是构成蜀恢527产量相关性状的关键基因。同时,整合文献报道产量相关性状的QTLs定位结果,也发现了一些可能解释关键区段影响产量相关性状的候选QTLs位点。
As one of the backbone parents currently used in hybrid rice breeding Shuhui 527 has many merits, such as high general combining ability, strong heterosis of hybrid combination, and many derivative R-lines. In order to clarify the genetic composition and the key genome regions of yield related characters of Shuhui 527, genomic scanning and QTLs analysis of Shuhui 527 were performed in this study. Main results were as the following:
1. The genetic composition and the key genome regions of yield related characters of Shuhui 527 were defined by genomic scanning and hereditas analysis of yield related traits.
(1). The results showed that seed-setting rate, filled grain number per panicle, grain number per panicle and panicles were possibly derived from the pedigree of IR24-Shuhui527; the weight of a thousand seeds, plant weight and panicles were possibly derived from the pedigree of Gui630-R1318-Shuhui 527.
(2).The genetic originated map of Shuhui 527 and its related ancestral parents were constructed by genomic scanning of materials in the pedigree with 1050 SSR primers. The results revealed that①the shared fragments of all varieties (i.e. none polymorphic fragments) accounted for 62.94%;②putative multi-originated fragments (polymorphic marker was unable to identify its origin) accounted for approximately 17.53%;③in the breeding process of Shuhui 527, R1318 had contributed 13.68% fragments, Fu36-2 had contributed 0.53% fragments, and IR24 had contributed 1.32% fragments;④Shuhui 527 had contributed 4% itself fragments.
(3). The key genome regions of Shuhui 527 was initially determined by the results of genomic scanning and hereditas analysis of yield related traits. Yield related key genormic regions of Shuhui527 were involved of those regions called Shuhui527 specific fragments, IR24 Originated fragments and R1318 originated fragments.
2. Using 288 G46B×Shuhui527 F2 descendants as mapping population, we constructed a rice SSR linkage map. By means of SSR linkage map, quantitative trait loci (QTLs) with 6 yield related traits including 1000-grain weight, Filled grain number per panicle, Grain number per panicle, seed setting rate, Pancile number, and Weight per plant were positioned and analyzed. Main results were as the following:
(1).244 SSR markers coming from 1895 SSR markers overlaying the rice genome had expressed polymorphism in both G46B and Shuhui527, polymorphism frequency was 12.88%.
(2).We constructed a molecular genetic map included 102 pairs of SSR markers which covered 2256.2 cM of rice genome, and the average distance between two markers spanned 22.12 cM with the population of G46BXShuhui527 F2. Two linkage groups of the chromosome 2 covered the longest (550.3cM) genome region, and the the linkage group of the chromosome 11 is the shortest (57.9 cM). The longest average distance between two markers spanned 34.1 cM and the shortest average distance between two markers spanned 14.48 cM, respectively. The linkage relationship of the markers was almost identical to previous studies.
(3). A total of 17 yield related QTLs were detected on chromosome 1,2, 4,5,7,8, respectively. Variation percentage explained by individual QTL ranged from 3.02% to 20.73%, out of which 5 QTLs explained more than 10% phenotypic variation and 3 QTLs explained less than 5% phenotypic variation. The detailed informations of 17 QTLs were as the following:
①Three QTLs were detected for 1000-grain weight, named qKGW-2-1, KGW-2-2 and qKGW-8-1. Totally, they explained 20.2% of the phenotypic variation. Among them, the qKGW-2-1 and qKGW-2-2 in the marker interval RM3316～RM3774 and RM3680～RM6853 of chromosome 2,accounting for 6.99% and 5.17% variation, respectively, the qKGW-8-1 were located in the marker interval RM1019-RM6925 of chromosome 8, accounting for 7.88% variation. The additive effects of qKGW-2-1 and qKGW-8-1 came from the male parent Shuhui527, however qKGW-2-2 came from the female parent G46B. The dominant effects of qKGW-2-1 and qKGW-8-1came from thefemale parent G46B, however qKGW-2-2 came from the male parent Shuhui527。
②Three QTLs were detected for filled grain number, named qFGP-1-1, qFGP-2-1, and qFGP-4-1. Totally, they explained 30.16% of the phenotypic variation. Among them, the qFGP-1-1 in the marker interval RM1003-RM8084 of chromosome 1, accounting for 9.30% variation, the qFGP-2-1 were located in the marker interval RM3692～RM208 of chromosome 2, accounting for 16.58% variation. the qFGP-4-1 in the marker interval RM8213～RM3658 of chromosome 4, accounting for 4.28% variation. The additive effects of qFGP-2-1 and qFGP-4-1 came from the male parent Shuhui527, however qFGP-1-1 came from the female parent G46B. The dominant effects of qFGP-1-land qFGP-2-1came from the female parent G46B, however qFGP-4-1came from the male parent Shuhui527。
③Two QTLs were detected for grain per panicle, named qGPP-2-land qGPP-4-1. Totally, they explained 10.13% of the phenotypic variation. Among them, the qGPP-2-1 in the marker interval RM3316-RM3774 of chromosome 2, accounting for 7.11% variation, the qGPP-4-1 were located in the marker interval RM7051～RM7187 of chromosome 4, accounting for 3.02% variation. The additive effects of qGPP-2-1 came from the male parent Shuhui527, however qGPP-4-1 came from the female parent G46B. The dominant effects of qGPP-2-land qGPP-4-1 came from thefemale parent G46B。
④Five QTLs were detected for seed setting rate, named qSS-1-1, qSS-2-1, qSS-7-1, qSS-7-2 and qSS-8-1. Totally, they explained 43.86% of the phenotypic variation. Among them, the qSS-1-1 in the marker interval RM5718- RM5919 of chromosome 1, accounting for 8.69% variation, the qSS-2-1 were located in the marker interval RM3692-RM208 of chromosome 2, accounting for 11.72% variation, the qSS-7-1 in the marker interval RM3831～RM5344 of chromosome 7, accounting for 7.92% variation. the qSS-7-2 were located in the marker interval RM3635～RM7110 of chromosome 7, accounting for 12.49% variation. the qSSS-1 were located in the marker interval RM7057-RM6010 of chromosome 8, accounting for 3.04% variation. The additive effects of qSS-1-1、qSS-2-land qSS-7-1 came from the male parent Shuhui527, however qSS-7-2 and qSSS-1 came from the female parent G46B. The dominant effects of qSS-7-2 came from the female parent G46B, however qSS-1-1 qSS-2-1、qSS-7-1 and qSS-8-1 came from the male parent Shuhui527。
⑤Two QTLs were detected for panicle number, named qPN-5-1 and qPN-8-1. Totally, they explained 25.89% of the phenotypic variation. Among them, the qPN-5-1 in the marker interval RM7653～RM3663 of chromosome 5, accounting for 5.16% variation, the qPN-8-1 were located in the marker interval RM4955-RM7057 of chromosome 8, accounting for 20.73% variation. The additive effects of qPN-5-land qPN-8-1 came from the female parent G46B. The dominant effects of qPN-5-land qPN-8-1 came from the female parent G46B.
⑥Two QTLs were detected for yield per plant, named qGYD-2-1 and qGYD-8-1. Totally, they explained 15.92% of the phenotypic variation. Among them, the qGYD-2-1 in the marker interval RM3355-RM6318 of chromosome 2, accounting for 5.34% variation, the qGYD-8-1 were located in the marker interval RM4955-RM7057 of chromosome 8, accounting for 10.58% variation. The additive effects of qGYD-2-1 came from the male parent Shuhui527, however qGYD-8-1 came from the female parent G46B. The dominant effects of qGYD-2-land qGYD-8-1 came from the female parent G46B.
(4) 288 F2 individuals derived from G46B and Shuhui527 were used to construct a genetic linkage map. Among the 131 markers,15 SSR markers, occupying 11.5% of the difference SSR markers showed genetic segregation distortion(P<0.05). RM5586, RM6554 and RM8121 inclined to the genotype of G46B;RM594、RM1092、RM5665、RM3308、RM20285 and RM336 inclined to the genotype of Shuhui527; RM6717, RM1339 and RM1364 inclined to the genotype of both G46B and Shuhui527,less heterozygous genotype;RM8240 and RM1384 inclined to the heterozygous genotype, less isozygoty genotype;RM3572 inclined to the genotype of both G46B and heterozygous genotype.
3 Candidate yield related QTLs in key fragments of Shuhui 527
The candidate QTLs of Shuhui 527 was initially determined by comparing the results of the key genomic fragments and the QTL locations and effects. Comparation suggested that qKGW-2-1、qKGW-2-2 and qKGW-8-1 for 1000-grain weight, qGYD-2-1 for weight per plant, qFGP-2-1 and qFGP-4-1 for filled grain number, qGPP-2-1 for grain per panicle, qSS-1-1、qSS-2-1、qSS-7-1 and qSS-8-1 for seed setting rate were candidate QTLs for the yield related traits of Shuhui 527.Besides, some other potential candidate QTLs were also discussed by integrating their genomic locations reported previously to the key genomic fragments of Shuhui 527.
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