水稻粒长基因qGL3的定位克隆、功能分析及育种利用研究
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摘要
水稻的单株产量是由穗数、每穗粒数和粒重三个因素共同决定的,其中粒重是由籽粒大小和灌浆程度共同决定。在灌浆程度理想的情况下,水稻的粒重可以直观地认为由水稻的籽粒大小决定。水稻籽粒的大小从外观上可以细分为籽粒长度、宽度和厚度三个组分,遗传上受数量性状基因座(QTLs, quantitative trait loci)控制,有较高的遗传率。水稻籽粒的长、宽、厚直接关系到水稻的籽粒大小,同时又决定着水稻的长宽比等外观品质性状,因而,对单子叶分子生物学研究的模式植物一水稻的粒形和粒重研究具有重要理论和实践意义。
本研究利用一个超大粒粳稻材料N411与N643、93-11、热研、龙里黑糯和苏旺往尔等5个籽粒大小和形状不同的水稻材料杂交,构建了5个F2分离群体。对这5个F2群体的遗传分析发现：超大粒材料与其他5个材料间存在控制籽粒大小和形状的丰富的遗传基础差异。对粒形和粒重等性状的相关性分析表明：籽粒的长度与宽度之间的相关性在群体间存在较大的差异,而粒长与粒厚及粒宽与粒厚均存在显著的相关性,同时粒长、粒宽和粒厚与粒重的相关性也均达到了极显著水平。
利用N411与小粒籼稻材料N643构建的F2群体,对控制水稻籽粒及穗部不同性状的QTL进行检测和定位,共检测到控制水稻4个籽粒性状和3个穗部性状的30个QTL位点。在第二染色体分子标记RM5350与RM6639之间检测到一个同时控制粒宽、粒厚和粒重的位点,此位点与已经克隆的GW2处于同一位置；在第三染色体分子标记RM3207与RM7370之间检测到一个同时控制粒长、粒厚、粒重和穗粒数的位点,此位点与已经克隆的GS3处于同一位置；在第五染色体分子标记RM5874和RM1237之间检测到一个同时控制粒宽和粒重的位点,在这一较大的区间内,有两个控制籽粒宽度的QTL位点已经被克隆,即qSW5/GW5和GS5；位于第三染色体分子标记RM6266与RM3350之间存在一个同时控制粒长、粒宽、粒厚、粒重和穗长的位点qGL3,该位点还未见报道,可能是控制粒长的一个新的主效位点。综合QTL的定位结果和对已报道的粒形基因在亲本间等位基因的分析比较发现：N411的超大粒形和粒重的遗传基础可能是累聚了至少四个已知的GS3、GW2、qSW5/GW5、 GS5和本文报道的qGL35个效应较大的正效应的粒形QTL位点。
针对粒长主效位点qGL3,以籼稻93-11作为轮回亲本进行连续回交,利用一个BC2F1自交获得的次级群体BC2F2,构建局部连锁图,再次确认了N411与93-11的组合中依然存在这个控制水稻粒长和粒重的主效位点qGL3。经过多次回交和自交之后,将这一位点分解为单个遗传因子,并分别构建了以93-11为背景的增效等位基因qg13和以N411为背景的减效等位基因qGL3的近等基因系：93-11NIL-qgl3和N411NIL-gGL3.对单因子分离后的分离群体的表型和基因型分析发现：qGL3是一个后代分离符合1：2：1的半显性位点。利用新开发的InDel标记对2,968个个体构成的N411×93-11BC2F3群体中获得的重组个体进行重组位点分析,结合后代表型测验,将qGL3定位在InDel标记XJ39与XJ26之间的46.6kb范围内。
通过基因组序列分析和表达分析比较,发现在该区间内有5个可能的ORFs,即：ORF1:LOC_Os03g44460;ORF2:LOC_Os03g44470;ORF3:LOC_Os03g44484;ORF4, LOC_Os03g44500和ORF5:LOC_Os03g44510。从中鉴定出唯一一个亲本间有差异的候选基因ORF4(LOC_Os03g44500),它编码一个包含两个Kelch结构域的丝氨酸/苏氨酸磷酸(酯)酶(OsPPKL1)。与93-11的OsPPKL193-11相比,来自N411的OsPPKL1N411的cDNA序列有四处单核苷酸变异SNP1-4：其中SNP1是位于+1092位置的C(93-11)转变为A(N411)(c.+1092C→A),导致编码蛋白的364位的天冬氨酸转变成了谷氨酸(D364E):SNP2是+1495位的C(93-11)转变成了T(N411)(c.+1495C→T),导致499位的组氨酸转变成了酪氨酸(H499Y)；另外两处SNP3和SNP4分别是c.+2643A→G和c.+2838T→C,这两个SNPs均是同义突变,不引起编码蛋白质的氨基酸的变化。生物信息学分析发现,在水稻中,OsPPKL1具有两个同源基因：OsPPKL2和OsPPKL3.结合其他多物种的同源基因比对发现,来自N411的等位基因OsPPKL1N411的突变位点SNP1发生在第二个Kelch结构域的一个保守的AVLDT区域,而突变位点SNP2位于一个非完全保守区域。
对三个同源基因的表达谱分析发现：OsPPKLs具有相似的表达模式,在幼穗中的表达量随着发育进程而逐渐增加,总体上,OsPPKL1和OsPPKL3的表达量高于OsPPKL2。OsPPKL1启动子的GUS活性分析结果与表达谱分析结果相似。对三个来自93-11的OsPPKLs同源蛋白和来自N411的OsPPKL1N411的亚细胞定位发现：OsPPKL1和OsPPKL3定位于细胞质和细胞核中,而OsPPKL2定位于细胞质中。OsPPKL1N411的突变并没有改变OsPPKL193-11的亚细胞定位。
通过对来自93-11和N411的不同等位基因的转基因研究发现：在水稻品种中花11中过表达OsPPKL193-11会引起水稻籽粒变短,而过量表达OsPPKL1N411并不会引起籽粒明显变化,说明等位基因OsPPKL1N411丢失了OsPPKL193-11的负调控功能,形成了较长的籽粒。对OsPPKL193-11的KeIch和PP2A功能域的分别过量表达的转基因发现,单独过量表达Kelch93-11引起籽粒的明显变短,而单独过量表达PP2A93-11不会引起籽粒变化,这说明OsPPKL193-11中的Kelch结构域是OsPPKL193-11发挥负调控功能的关键结构域。对OsPPKL1的同源基因的过表达转基因发现：与OsPPKL193-11较近的同源基因OSPPKL3的过量表达同样引起水稻籽粒变短,而另外一个同源基因OsPPKL2的过量表达引起籽粒变长。对水稻品种东津(Dongjin)背景下分别敲除OSPPKLS基因家族的突变体的分析发现：Osppkl1和Osppkl3与野生型相比形成较长的籽粒,而Osppkl2形成较短的籽粒。综合转基因试验结果和突变体数据,推测OSPPKL1和OSPPKL3在水稻籽粒长短发育中发挥负调控功能,这种负调控功能来自其Kelch结构域；而OsPPKL2在水稻籽粒发育中发挥正调控的功能。
对93-11背景下功能型和非功能型的GS3和qGL3的不同等位基因的四种组合方式(GS3/qGL3,gs3/qGL3,GS3/qg13和gs3/qgl3)(?)勺近等基因系研究发现：在功能型GS3的背景下,单独的qGL3转变到ggl3引起籽粒长度的增加值(+2.7mm)大于在非功能性gs3背景下单独的qGL3转变到ggl3引起的籽粒长度的增加值(+2.0mm)。这说明：qgl3和gs3之间可能是部分加性的。进一步通过对这些近等基因系幼穗的表达谱芯片分析发现,qGL3和GS3调控的基因具有各自独立的,同时又有部分重叠的,其中它们共同调控的基因,在调控效果上有程度上的差异。
利用93-11背景下的近等基因系93-11NIL-qgl3和N411背景下的近等基因系N411NIL-qGL3对qGL3生物学功能的分析发现：qgl3是通过加快颖壳细胞的纵向分裂速度,在颖壳的纵向上形成更多的细胞而引起籽粒变长的；同时,qgl3可以增加子房的伸长速度和籽粒的灌浆速度。利用93-11NIL-qgl3进行育种利用研究发现,在田间试验中,在93-11背景下,导入纯合状态的ggl3可以在不显著改变株高、分蘖数、穗粒数、抽穗期和垩白率等其他农艺性状的情况下,通过增加粒长引起粒重增加,提高产量大约16.20%。鉴于qGL3是半显性遗传,利用93-11NIL-qgl3与三个光敏不育系配制两系杂交稻,与利用93-11配制的杂交稻组合对比发现,处于杂合状态的qgl3可以提高产量约10.12%～13.48%。
对94个粒形丰富性极高的水稻核心种质的qGL3区域,包含SNP1-4的3.6kb的基因组序列进行分析,鉴定到25个多态性位点。利用这些多态性位点结合籽粒长度数据的关联分析发现：突变SNP1是一个稀有变异,与粒长具有显著关联,而SNP2虽然引起氨基酸的变化,但是与其他同义突变或者内含子区的多态性位点类似,是籼粳稻中广泛存在的差异,与粒长没有显著的关联。结合对水稻核心种质中报道的其他粒形基因的等位基因分析,讨论了自然群体中水稻已知粒形基因的等位分布情况和水稻粒形的遗传结构。
Grain number, panicle number and grain weight are three important components of grain yield of rice (Oryza saliva L.). When grain number per panicle and panicle number per plant reach an ideal level, improvement of grain weight plays a key role in further yield increase in rice breeding program. Grain weight is largely determined by grain size, which is specified by its three dimensions (grain length, width, and thickness) and the degree of filling. Meanwhile, grain shape is also a quality trait for rice so that study on grain size or weight in model plant rice is of great economic and academic meaning.
For a better understanding of the genetic characteristics of rice grain size or weight, we screened an extra-large grain japonica accession, N411, with more than7.0grams of100-grain weight (HGW) and constructed five F2populations with five small-grain accessions (N643,93-11, RY, LLHN and SWWR). Genetic analysis of the grain shape and weight traits with those five F2populations indicates that there are many genetic differences between the extra-large grain N411and the other five small-grain accessions. The quantitative trait loci (QTL) for four grain traits and three panicle traits were analyzed in the N411×N643F2population. A total of30QTL for the seven traits were detected, including four QTLs for grain length (GL) on chromosome3,10and11; four for grain width (GW) on chromosome2,3and5; eight for grain thickness (GT) on chromosome2,3,5and6; seven for100-grain weight (HGW) on chromosome2,3,5,6,10and11; two for spikelete per panicle (SPP) on chromosome1and3; three for panicle length on chromosome2,3and6; two for grain rate on chromosome7and8. Most of the QTLs for grain traits were mapped to nearly the same intervals or adjacent regions. These pleiotropic performances provided satisfactory explanations for the results of high phenotypic correlations between grain traits in the F2population. Compared with previous studies, the mapping regions of the major QTL qGL3a, qGW2.2and qGW5, explaining25.54%,50.63%and15.38%of the phenotypic variation, were coincident with those of cloned genes GS3, GW2and qSW5/GW5, respectively. qSPP1, which positive alleles from line N643, was localized to the same interval of the cloned gene Gnla. A new grain length QTL, qGL3, which explained38.38%of the total variation of grain length, was mapped to the interval of RM5864-RM3199on the long arm of chromosome3, where the QTLs for GW, GT, HGW and PL were also detected. That most of the positive QTL for the grain traits came from N411provided a genetic explanation for the mechanism of the extra-large grain formation in N411.
The novel major grain length QTL, qGL3, which explained variations for38.38%grain length,5.96%width,11.89%thickness and27.99%weight, was further disassembled to a single genetic factor in the background of indica accession93-11with marker-associated selection and successive backcrosses. Using a BC2F3population and BC2F4progeny testing, the qGL3QTL was mapped to a46.6-kb region with five predicted ORFs (ORF1, LOC_Os03g44460; ORF2, LOC_Os03g44470; ORF3, LOC_Os03g44484; ORF4, LOC_Os03g44500, and ORF5, LOC_Os03g44510)(Nipponbare genome sequence as a reference).
Based on RT-PCR analysis and EST information, we found that only ORF3and ORF4were expressed, while ORF1and ORF2encoding retrotransposon proteins and ORF5encoding a transposon were not expressed in rice. RT-PCR analyses showed no expressional difference of ORF3and ORF4in young panicles between93-11and its near-isogenic line (NIL)93-11NIL-qgl3. Sequence comparison of these two expressed ORFs between93-11and N411revealed no difference in the ORF3sequence and four SNPs in the ORF4. SNP1, a single nucleotide transition from C (93-11) to A (N411)(c.+1092C→A), is present in the10th exon of the ORF4, and SNP2, a single nucleotide transition from C (93-11) to T (N411)(c.+1495C→T), in the11th exon. These two transitions cause amino acid residue changes from aspartate to glutamate (Asp364Glu) and histidine to tyrosine (His499Tyr), respectively. SNP3(c.+2643A->G, in the18th exon) and SNP4(c.+2838T→C, in the21th exon) do not cause amino acid residue changes. Therefore, ORF4was most likely the candidate gene for qGL3.
The ORF4encodes a putative phosphatase with two Kelch repeat domains (OsPPKL1). There are two OsPPKL1homologues, OsPPKL2and OsPPKL3, in rice genome. Sequence alignment of plant homologues of OsPPKL1showed that the amino acid transition (Asp364Glu) caused by SNP1in OsPPKLlN411occurs in a conserved AVLDT motif of the second Kelch domain while the transition (His499Tyr) caused by SNP2occurs in a non-conserved region. Transgenic analysis found that over-expression of OsPPKL193-11and its closer homologue OsPPKL3forms shorter grains in Zhonghua11while over-expression of the other homologue OsPPKL2forms longer grains. Over-expression of the peptide cutoff PP2A domain forms shorter grains but over-expression the peptide without the two Kelch domains causes no effect on rice grain. Accordingly, the T-DNA insertion mutant of OsPPKLI and OsPPKL3exhibits longer grains and mutant of OsPPKL2exhibits shorter grains as compared with its wild type accession Dongjin. Those data indicated that OsPPKLI and its closer homologue OsPPKL3function as negative regulators of grain length, while OsPPKL2as a positive regulator. The Kelch domain is essential for OsPPKL193-11nagetive function.
In the93-11genetic background,(NIL-GS3/qGL3), single loss qGL3increase grain length much more (～2.7mm) than single loss of GS3(～1.7mm), and loss of qGL3plus GS3together showed partially additive function (～3.7mm). And loss of qGL3in the functional GS3background could increase grain (2.7mm) more than in the null gs3background (～2.0mm). These data indicated that GS3and qGL3take in partially together in rice grain regulation. Some genes were overlapped and in different levels regulated by those two genes indicated by microarray.
The near-isogenic line in the93-11background analysis indicated that the long glumes of93-11NIL-qgl3resulted from an increase in cell numbers longitudinally, which was consistent with the observation that the ovaries elongation of93-11NIL-qgl3was faster than93-11. Comparison of grain yield and other agronomic traits between93-11and N\L-qgl3showed that qgl3increased grain weight (+37.03%), length (+19.69%), width (+1.15%) and thickness (+8.26%) without changing other agronomic traits significantly. The heterozygote could increase grain weight about16.24%. The qgl3allele can increase16%of grain yield in inbred rice, and10%～13%in hybrid rice by regulating grain length, weight and filling rate.
Ninety-four rice germplasms with abundant diversity in grain size were selected for sequencing a3.6-kb genomic DNA fragment that covers the four mutation sites of the qgl3. We found only one variety, DT108(grain length=12.08mm) have the same SNP1as N411, while polymorphisms of SNP2, SNP3and SNP4are widely distributed in either japonica or indica varieties. By association analysis of the SNPs and InDel markers in the3.6-kb region with grain length of the94germplasms, we found that SNP1had a high contribution to grain length while other polymorphic sites had no significant contributions to grain length. These results indicate that the qgl3is a rare allele in rice and SNP1is a functional mutation for long grain. Using this collection, the gene alleles of the reported grain shape genes/QTLs were analyzed, and the genetic architecture of rice grain shape was discussed.
Those results indicated that qGL3may be used in either cross-selection breeding by MAS, or hybrid-rice breeding to increase rice yield and to improve appearance quality. Breeding application of this rare and desirable allele for extra-large grain may make a great improvement in the rice yield.
本研究利用一个超大粒粳稻材料N411与N643、93-11、热研、龙里黑糯和苏旺往尔等5个籽粒大小和形状不同的水稻材料杂交,构建了5个F2分离群体。对这5个F2群体的遗传分析发现：超大粒材料与其他5个材料间存在控制籽粒大小和形状的丰富的遗传基础差异。对粒形和粒重等性状的相关性分析表明：籽粒的长度与宽度之间的相关性在群体间存在较大的差异,而粒长与粒厚及粒宽与粒厚均存在显著的相关性,同时粒长、粒宽和粒厚与粒重的相关性也均达到了极显著水平。
利用N411与小粒籼稻材料N643构建的F2群体,对控制水稻籽粒及穗部不同性状的QTL进行检测和定位,共检测到控制水稻4个籽粒性状和3个穗部性状的30个QTL位点。在第二染色体分子标记RM5350与RM6639之间检测到一个同时控制粒宽、粒厚和粒重的位点,此位点与已经克隆的GW2处于同一位置；在第三染色体分子标记RM3207与RM7370之间检测到一个同时控制粒长、粒厚、粒重和穗粒数的位点,此位点与已经克隆的GS3处于同一位置；在第五染色体分子标记RM5874和RM1237之间检测到一个同时控制粒宽和粒重的位点,在这一较大的区间内,有两个控制籽粒宽度的QTL位点已经被克隆,即qSW5/GW5和GS5；位于第三染色体分子标记RM6266与RM3350之间存在一个同时控制粒长、粒宽、粒厚、粒重和穗长的位点qGL3,该位点还未见报道,可能是控制粒长的一个新的主效位点。综合QTL的定位结果和对已报道的粒形基因在亲本间等位基因的分析比较发现：N411的超大粒形和粒重的遗传基础可能是累聚了至少四个已知的GS3、GW2、qSW5/GW5、 GS5和本文报道的qGL35个效应较大的正效应的粒形QTL位点。
针对粒长主效位点qGL3,以籼稻93-11作为轮回亲本进行连续回交,利用一个BC2F1自交获得的次级群体BC2F2,构建局部连锁图,再次确认了N411与93-11的组合中依然存在这个控制水稻粒长和粒重的主效位点qGL3。经过多次回交和自交之后,将这一位点分解为单个遗传因子,并分别构建了以93-11为背景的增效等位基因qg13和以N411为背景的减效等位基因qGL3的近等基因系：93-11NIL-qgl3和N411NIL-gGL3.对单因子分离后的分离群体的表型和基因型分析发现：qGL3是一个后代分离符合1：2：1的半显性位点。利用新开发的InDel标记对2,968个个体构成的N411×93-11BC2F3群体中获得的重组个体进行重组位点分析,结合后代表型测验,将qGL3定位在InDel标记XJ39与XJ26之间的46.6kb范围内。
通过基因组序列分析和表达分析比较,发现在该区间内有5个可能的ORFs,即：ORF1:LOC_Os03g44460;ORF2:LOC_Os03g44470;ORF3:LOC_Os03g44484;ORF4, LOC_Os03g44500和ORF5:LOC_Os03g44510。从中鉴定出唯一一个亲本间有差异的候选基因ORF4(LOC_Os03g44500),它编码一个包含两个Kelch结构域的丝氨酸/苏氨酸磷酸(酯)酶(OsPPKL1)。与93-11的OsPPKL193-11相比,来自N411的OsPPKL1N411的cDNA序列有四处单核苷酸变异SNP1-4：其中SNP1是位于+1092位置的C(93-11)转变为A(N411)(c.+1092C→A),导致编码蛋白的364位的天冬氨酸转变成了谷氨酸(D364E):SNP2是+1495位的C(93-11)转变成了T(N411)(c.+1495C→T),导致499位的组氨酸转变成了酪氨酸(H499Y)；另外两处SNP3和SNP4分别是c.+2643A→G和c.+2838T→C,这两个SNPs均是同义突变,不引起编码蛋白质的氨基酸的变化。生物信息学分析发现,在水稻中,OsPPKL1具有两个同源基因：OsPPKL2和OsPPKL3.结合其他多物种的同源基因比对发现,来自N411的等位基因OsPPKL1N411的突变位点SNP1发生在第二个Kelch结构域的一个保守的AVLDT区域,而突变位点SNP2位于一个非完全保守区域。
对三个同源基因的表达谱分析发现：OsPPKLs具有相似的表达模式,在幼穗中的表达量随着发育进程而逐渐增加,总体上,OsPPKL1和OsPPKL3的表达量高于OsPPKL2。OsPPKL1启动子的GUS活性分析结果与表达谱分析结果相似。对三个来自93-11的OsPPKLs同源蛋白和来自N411的OsPPKL1N411的亚细胞定位发现：OsPPKL1和OsPPKL3定位于细胞质和细胞核中,而OsPPKL2定位于细胞质中。OsPPKL1N411的突变并没有改变OsPPKL193-11的亚细胞定位。
通过对来自93-11和N411的不同等位基因的转基因研究发现：在水稻品种中花11中过表达OsPPKL193-11会引起水稻籽粒变短,而过量表达OsPPKL1N411并不会引起籽粒明显变化,说明等位基因OsPPKL1N411丢失了OsPPKL193-11的负调控功能,形成了较长的籽粒。对OsPPKL193-11的KeIch和PP2A功能域的分别过量表达的转基因发现,单独过量表达Kelch93-11引起籽粒的明显变短,而单独过量表达PP2A93-11不会引起籽粒变化,这说明OsPPKL193-11中的Kelch结构域是OsPPKL193-11发挥负调控功能的关键结构域。对OsPPKL1的同源基因的过表达转基因发现：与OsPPKL193-11较近的同源基因OSPPKL3的过量表达同样引起水稻籽粒变短,而另外一个同源基因OsPPKL2的过量表达引起籽粒变长。对水稻品种东津(Dongjin)背景下分别敲除OSPPKLS基因家族的突变体的分析发现：Osppkl1和Osppkl3与野生型相比形成较长的籽粒,而Osppkl2形成较短的籽粒。综合转基因试验结果和突变体数据,推测OSPPKL1和OSPPKL3在水稻籽粒长短发育中发挥负调控功能,这种负调控功能来自其Kelch结构域；而OsPPKL2在水稻籽粒发育中发挥正调控的功能。
对93-11背景下功能型和非功能型的GS3和qGL3的不同等位基因的四种组合方式(GS3/qGL3,gs3/qGL3,GS3/qg13和gs3/qgl3)(?)勺近等基因系研究发现：在功能型GS3的背景下,单独的qGL3转变到ggl3引起籽粒长度的增加值(+2.7mm)大于在非功能性gs3背景下单独的qGL3转变到ggl3引起的籽粒长度的增加值(+2.0mm)。这说明：qgl3和gs3之间可能是部分加性的。进一步通过对这些近等基因系幼穗的表达谱芯片分析发现,qGL3和GS3调控的基因具有各自独立的,同时又有部分重叠的,其中它们共同调控的基因,在调控效果上有程度上的差异。
利用93-11背景下的近等基因系93-11NIL-qgl3和N411背景下的近等基因系N411NIL-qGL3对qGL3生物学功能的分析发现：qgl3是通过加快颖壳细胞的纵向分裂速度,在颖壳的纵向上形成更多的细胞而引起籽粒变长的；同时,qgl3可以增加子房的伸长速度和籽粒的灌浆速度。利用93-11NIL-qgl3进行育种利用研究发现,在田间试验中,在93-11背景下,导入纯合状态的ggl3可以在不显著改变株高、分蘖数、穗粒数、抽穗期和垩白率等其他农艺性状的情况下,通过增加粒长引起粒重增加,提高产量大约16.20%。鉴于qGL3是半显性遗传,利用93-11NIL-qgl3与三个光敏不育系配制两系杂交稻,与利用93-11配制的杂交稻组合对比发现,处于杂合状态的qgl3可以提高产量约10.12%～13.48%。
对94个粒形丰富性极高的水稻核心种质的qGL3区域,包含SNP1-4的3.6kb的基因组序列进行分析,鉴定到25个多态性位点。利用这些多态性位点结合籽粒长度数据的关联分析发现：突变SNP1是一个稀有变异,与粒长具有显著关联,而SNP2虽然引起氨基酸的变化,但是与其他同义突变或者内含子区的多态性位点类似,是籼粳稻中广泛存在的差异,与粒长没有显著的关联。结合对水稻核心种质中报道的其他粒形基因的等位基因分析,讨论了自然群体中水稻已知粒形基因的等位分布情况和水稻粒形的遗传结构。
Grain number, panicle number and grain weight are three important components of grain yield of rice (Oryza saliva L.). When grain number per panicle and panicle number per plant reach an ideal level, improvement of grain weight plays a key role in further yield increase in rice breeding program. Grain weight is largely determined by grain size, which is specified by its three dimensions (grain length, width, and thickness) and the degree of filling. Meanwhile, grain shape is also a quality trait for rice so that study on grain size or weight in model plant rice is of great economic and academic meaning.
For a better understanding of the genetic characteristics of rice grain size or weight, we screened an extra-large grain japonica accession, N411, with more than7.0grams of100-grain weight (HGW) and constructed five F2populations with five small-grain accessions (N643,93-11, RY, LLHN and SWWR). Genetic analysis of the grain shape and weight traits with those five F2populations indicates that there are many genetic differences between the extra-large grain N411and the other five small-grain accessions. The quantitative trait loci (QTL) for four grain traits and three panicle traits were analyzed in the N411×N643F2population. A total of30QTL for the seven traits were detected, including four QTLs for grain length (GL) on chromosome3,10and11; four for grain width (GW) on chromosome2,3and5; eight for grain thickness (GT) on chromosome2,3,5and6; seven for100-grain weight (HGW) on chromosome2,3,5,6,10and11; two for spikelete per panicle (SPP) on chromosome1and3; three for panicle length on chromosome2,3and6; two for grain rate on chromosome7and8. Most of the QTLs for grain traits were mapped to nearly the same intervals or adjacent regions. These pleiotropic performances provided satisfactory explanations for the results of high phenotypic correlations between grain traits in the F2population. Compared with previous studies, the mapping regions of the major QTL qGL3a, qGW2.2and qGW5, explaining25.54%,50.63%and15.38%of the phenotypic variation, were coincident with those of cloned genes GS3, GW2and qSW5/GW5, respectively. qSPP1, which positive alleles from line N643, was localized to the same interval of the cloned gene Gnla. A new grain length QTL, qGL3, which explained38.38%of the total variation of grain length, was mapped to the interval of RM5864-RM3199on the long arm of chromosome3, where the QTLs for GW, GT, HGW and PL were also detected. That most of the positive QTL for the grain traits came from N411provided a genetic explanation for the mechanism of the extra-large grain formation in N411.
The novel major grain length QTL, qGL3, which explained variations for38.38%grain length,5.96%width,11.89%thickness and27.99%weight, was further disassembled to a single genetic factor in the background of indica accession93-11with marker-associated selection and successive backcrosses. Using a BC2F3population and BC2F4progeny testing, the qGL3QTL was mapped to a46.6-kb region with five predicted ORFs (ORF1, LOC_Os03g44460; ORF2, LOC_Os03g44470; ORF3, LOC_Os03g44484; ORF4, LOC_Os03g44500, and ORF5, LOC_Os03g44510)(Nipponbare genome sequence as a reference).
Based on RT-PCR analysis and EST information, we found that only ORF3and ORF4were expressed, while ORF1and ORF2encoding retrotransposon proteins and ORF5encoding a transposon were not expressed in rice. RT-PCR analyses showed no expressional difference of ORF3and ORF4in young panicles between93-11and its near-isogenic line (NIL)93-11NIL-qgl3. Sequence comparison of these two expressed ORFs between93-11and N411revealed no difference in the ORF3sequence and four SNPs in the ORF4. SNP1, a single nucleotide transition from C (93-11) to A (N411)(c.+1092C→A), is present in the10th exon of the ORF4, and SNP2, a single nucleotide transition from C (93-11) to T (N411)(c.+1495C→T), in the11th exon. These two transitions cause amino acid residue changes from aspartate to glutamate (Asp364Glu) and histidine to tyrosine (His499Tyr), respectively. SNP3(c.+2643A->G, in the18th exon) and SNP4(c.+2838T→C, in the21th exon) do not cause amino acid residue changes. Therefore, ORF4was most likely the candidate gene for qGL3.
The ORF4encodes a putative phosphatase with two Kelch repeat domains (OsPPKL1). There are two OsPPKL1homologues, OsPPKL2and OsPPKL3, in rice genome. Sequence alignment of plant homologues of OsPPKL1showed that the amino acid transition (Asp364Glu) caused by SNP1in OsPPKLlN411occurs in a conserved AVLDT motif of the second Kelch domain while the transition (His499Tyr) caused by SNP2occurs in a non-conserved region. Transgenic analysis found that over-expression of OsPPKL193-11and its closer homologue OsPPKL3forms shorter grains in Zhonghua11while over-expression of the other homologue OsPPKL2forms longer grains. Over-expression of the peptide cutoff PP2A domain forms shorter grains but over-expression the peptide without the two Kelch domains causes no effect on rice grain. Accordingly, the T-DNA insertion mutant of OsPPKLI and OsPPKL3exhibits longer grains and mutant of OsPPKL2exhibits shorter grains as compared with its wild type accession Dongjin. Those data indicated that OsPPKLI and its closer homologue OsPPKL3function as negative regulators of grain length, while OsPPKL2as a positive regulator. The Kelch domain is essential for OsPPKL193-11nagetive function.
In the93-11genetic background,(NIL-GS3/qGL3), single loss qGL3increase grain length much more (～2.7mm) than single loss of GS3(～1.7mm), and loss of qGL3plus GS3together showed partially additive function (～3.7mm). And loss of qGL3in the functional GS3background could increase grain (2.7mm) more than in the null gs3background (～2.0mm). These data indicated that GS3and qGL3take in partially together in rice grain regulation. Some genes were overlapped and in different levels regulated by those two genes indicated by microarray.
The near-isogenic line in the93-11background analysis indicated that the long glumes of93-11NIL-qgl3resulted from an increase in cell numbers longitudinally, which was consistent with the observation that the ovaries elongation of93-11NIL-qgl3was faster than93-11. Comparison of grain yield and other agronomic traits between93-11and N\L-qgl3showed that qgl3increased grain weight (+37.03%), length (+19.69%), width (+1.15%) and thickness (+8.26%) without changing other agronomic traits significantly. The heterozygote could increase grain weight about16.24%. The qgl3allele can increase16%of grain yield in inbred rice, and10%～13%in hybrid rice by regulating grain length, weight and filling rate.
Ninety-four rice germplasms with abundant diversity in grain size were selected for sequencing a3.6-kb genomic DNA fragment that covers the four mutation sites of the qgl3. We found only one variety, DT108(grain length=12.08mm) have the same SNP1as N411, while polymorphisms of SNP2, SNP3and SNP4are widely distributed in either japonica or indica varieties. By association analysis of the SNPs and InDel markers in the3.6-kb region with grain length of the94germplasms, we found that SNP1had a high contribution to grain length while other polymorphic sites had no significant contributions to grain length. These results indicate that the qgl3is a rare allele in rice and SNP1is a functional mutation for long grain. Using this collection, the gene alleles of the reported grain shape genes/QTLs were analyzed, and the genetic architecture of rice grain shape was discussed.
Those results indicated that qGL3may be used in either cross-selection breeding by MAS, or hybrid-rice breeding to increase rice yield and to improve appearance quality. Breeding application of this rare and desirable allele for extra-large grain may make a great improvement in the rice yield.
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