Identification of QTLs for Yield and Associated Traits in F₂ Population of Rice

Identification of quantitative trait loci (QTLs) controlling yield and yield-related traits in rice was performed in the F₂ mapping population derived from parental rice genotypes DHMAS and K343. A total of 30 QTLs governing nine different traits were identified using the composite interval mapping (CIM) method. Four QTLs were mapped for number of tillers per plant on chromosomes 1 (2 QTLs), 2 and 3; three QTLs for panicle number per plant on chromosomes 1 (2 QTLs) and 3; four QTLs for plant height on chromosomes 2, 4, 5 and 6; one QTL for spikelet density on chromosome 5; four QTLs for spikelet fertility percentage (SFP) on chromosomes 2, 3 and 5 (2 QTLs); two QTLs for grain length on chromosomes 1 and 8; three QTLs for grain width on chromosomes1, 3 and 8; three QTLs for 1000-grain weight (TGW) on chromosomes 1, 4 and 8 and six QTLs for yield per plant (YPP) on chromosomes 2 (3 QTLs), 4, 6 and 8. Most of the QTLs were detected on chromosome 2, so further studies on chromosome 2 could help unlock some new chapters of QTL for this cross of rice variety. Identified QTLs elucidating high phenotypic variance can be used for marker-assisted selection (MAS) breeding. Further, the exploitation of information regarding molecular markers tightly linked to QTLs governing these traits will facilitate future crop improvement strategies in rice.     

Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.)

Harvest index is a measure of success in partitioning assimilated photosynthate. An improvement of harvest index means an increase in the economic portion of the plant. Our objective was to identify genetic markers associated with harvest index traits using 203 O. sativa accessions. The phenotyping for 14 traits was conducted in both temperate (Arkansas) and subtropical (Texas) climates and the genotyping used 154 SSRs and an indel marker. Heading, plant height and weight, and panicle length had negative correlations, while seed set and grain weight/panicle had positive correlations with harvest index across both locations. Subsequent genetic diversity and population structure analyses identified five groups in this collection, which corresponded to their geographic origins. Model comparisons revealed that different dimensions of principal components analysis (PCA) affected harvest index traits for mapping accuracy, and kinship did not help. In total, 36 markers in Arkansas and 28 markers in Texas were identified to be significantly associated with harvest index traits. Seven and two markers were consistently associated with two or more harvest index correlated traits in Arkansas and Texas, respectively. Additionally, four markers were constitutively identified at both locations, while 32 and 24 markers were identified specifically in Arkansas and Texas, respectively. Allelic analysis of four constitutive markers demonstrated that allele 253 bp of RM431 had significantly greater effect on decreasing plant height, and 390 bp of RM24011 had the greatest effect on decreasing panicle length across both locations. Many of these identified markers are located either nearby or flanking the regions where the QTLs for harvest index have been reported. Thus, the results from this association mapping study complement and enrich the information from linkage-based QTL studies and will be the basis for improving harvest index directly and indirectly in rice.     

Association mapping of grain color,phenolic content,flavonoid content and antioxidant capacity in dehulled rice

Phytochemicals such as phenolics and flavonoids in rice grain are antioxidants that are associated with reduced risk of developing chronic diseases including cardiovascular disease, type-2 diabetes and some cancers. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. Association mapping based on linkage disequilibrium has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, genome-wide association mapping using models controlling both population structure (Q) and relative kinship (K) were performed to identify the marker loci/QTLs underlying the naturally occurring variations of grain color and nutritional quality traits in 416 rice germplasm accessions including red and black rice. A total of 41 marker loci were identified for all the traits, and it was confirmed that Ra (i.e., Prp-b for purple pericarp) and Rc (brown pericarp and seed coat) genes were main-effect loci for rice grain color and nutritional quality traits. RM228, RM339, fgr (fragrance gene) and RM316 were important markers associated with most of the traits. Association mapping for the traits of the 361 white or non-pigmented rice accessions (i.e., excluding the red and black rice) revealed a total of 11 markers for four color parameters, and one marker (RM346) for phenolic content. Among them, Wx gene locus was identified for the color parameters of lightness (L*), redness (a*) and hue angle (H ^o). Our study suggested that the markers identified in this study can feasibly be used to improve nutritional quality or health benefit properties of rice by marker-assisted selection if the co-segregations of the marker–trait associations are validated in segregating populations.     

直播条件下水稻6个穗部性状的QTL分析

在大田直播条件下,利用来源于＂Lemont/特青＂的重组自交系群体,对水稻6个穗部性状及其相互间遗传相关的分子基础进行了QTL分析,共检测到19个QTL,各性状QTL数为2～4个,单个QTL贡献率为4%～22%。共检测到3个染色体区段能同时影响多个穗部性状,其中第1染色体RM212-RM104和第2染色体RM263-RM221区段的QTL能同时影响单株产量、每穗颖花数、着粒密度和二次枝梗数中的3个或4个性状,且这2个区段的QTL对各性状的效应方向相同,增效等位基因均来自‘特青’,为各性状间表型正相关提供了重要的遗传解释。第11染色体RG1022附近的QTL对着粒密度的效应值为负,来自‘特青’的等位基因增加性状值,而对穗长的效应值为正,来自‘特青’的等位基因降低性状值,为这2个性状间表型负相关也提供了一定的遗传解释。此外,对水稻穗部性状QTL在多种环境和遗传背景下的稳定表达及其在分子标记辅助育种中的应用进行了讨论。     

Epistasis for Three Grain Yield Components in Rice (Oryza Sativa L.)

The genetic basis for three grain yield components of rice, 1000 kernel weight (KW), grain number per panicle (GN), and grain weight per panicle (GWP), was investigated using restriction fragment length polymorphism markers and F(4) progeny testing from a cross between rice subspecies japonica (cultivar Lemont from USA) and indica (cv. Tequing from China). Following identification of 19 QTL affecting these traits, we investigated the role of epistasis in genetic control of these phenotypes. Among 63 markers distributed throughout the genome that appeared to be involved in 79 highly significant (P < 0.001) interactions, most (46 or 73%) did not appear to have ``main'''' effects on the relevant traits, but influenced the trait(s) predominantly through interactions. These results indicate that epistasis is an important genetic basis for complex traits such as yield components, especially traits of low heritability such as GN and GWP. The identification of epistatic loci is an important step toward resolution of discrepancies between quantitative trait loci mapping and classical genetic dogma, contributes to better understanding of the persistence of quantitative genetic variation in populations, and impels reconsideration of optimal mapping methodology and marker-assisted breeding strategies for improvement of complex traits.     

Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.))

Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection.     

Quantitative trait loci for rice yield-related traits using recombinant inbred lines derived from two diverse cultivars

The thousand-grain weight and spikelets per panicle directly contribute to rice yield. Heading date and plant height also greatly influence the yield. Dissection of genetic bases of yield-related traits would provide tools for yield improvement. In this study, quantitative trait loci (QTL) mapping for spikelets per panicle, thousand-grain weight, heading date and plant height was performed using recombinant inbred lines derived from a cross between two diverse cultivars, Nanyangzhan and Chuan7. In total, 20 QTLs were identified for four traits. They were located to 11 chromosomes except on chromosome 4. Seven and five QTLs were detected for thousand-grain weight and spikelets per panicle, respectively. Four QTLs were identified for both heading date and plant height. About half the QTLs were commonly detected in both years, 2006 and 2007. Six QTLs are being reported for the first time. Two QTL clusters were identified in regions flanked by RM22065 and RM5720 on chromosome 7 and by RM502 and RM264 on chromosome 8, respectively. The parent, Nanyangzhan with heavy thousand-grain weight, carried alleles with increased effects on all seven thousand-grain weight QTL, which explained why there was no transgressive segregation for thousand-grain weight in the population. In contrast, Chuan7 with more spikelets per panicle carried positive alleles at all five spikelets per panicle QTL except qspp5. Further work on distinction between pleiotropic QTL and linked QTL is needed in two yield-related QTL clusters.     

Association mapping validates previously identified quantitative trait loci for salt tolerance in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Salinity is the main abiotic stress that limits rice (Oryza sativa L.) production worldwide. An association mapping project was designed to validate quantitative trait loci (QTLs) in rice associated with Na⁺, K⁺ and Ca⁺⁺ accumulation traits identified in our previous study of linkage mapping. Twenty four varieties/lines of rice were phenotyped for biochemical and yield traits. Among these varieties/lines, two mapping parents, Pokkali and IR-36, of our previous linkage mapping study were also included. For marker-trait assessments, both general linear model (GLM) and mixed linear model (MLM) analyses were performed. Thirteen significant marker-trait associations at P ≤ 0.001 were identified. Associated markers for these marker-trait associations were RM503, RM225, RM152, and RM254 located on chromosomes 3, 6, 8, and 11, respectively. Previously identified QTLs in linkage mapping study for Na⁺ uptake, Ca⁺⁺ uptake, total cations uptake, Ca⁺⁺ uptake ratio, K⁺ uptake ratio, and Na⁺/K⁺ uptake were validated in this study. Heritability values for these traits ranged from 1.00e-05 to 1. Linked markers for these validated QTLs were RM140, RM243, RM203, RM480, RM137, and RM254 located on chromosomes 1, 1, 3, 5, 8, and 11, respectively. These markers will be a valuable resource for marker-assisted breeding (MAB) approach to develop elite salt tolerant rice cultivars. This study demonstrates the potential of association mapping approach to validate previously identified QTLs.     

Clustered QTL for source leaf size and yield traits in rice (Oryza sativa L.)

Improvement of plant type plays an important role in super-high yield breeding in rice (Oryza sativa L.). In the present study, a set of backcross recombinant inbred lines derived from a cross of 9311 and Zhenshan97, both elite indica hybrid parents, were developed to identify quantitative trait loci (QTL) for flag leaf size, panicle and yield traits. Forty-seven QTL for 14 traits were detected in common in the two environmental trials, of which nine genomic regions contained clustered QTL affecting plant type traits and yield traits. Four co-localized QTL on chromosomes 1, 6, 7 and 8 involving QTL for flag leaf size (flag leaf length, width and area) contained the QTL for yield traits such as panicle weight (PW) and secondary branch number (SBN), and in all cases alleles from 9311 increased source leaf size and were associated with increased sink size and yield (SBN and PW). Using a subset of overlapping substitution lines for the QTL region on chromosome 1, the QTL were validated and narrowed into a 990?kbp interval (RM3746?CRM10435) with pleiotropic effects on flag leaf size, PW, SBN and spikelet number per panicle. These QTL clusters with large effects on source leaf size and yield-related traits provide good targets for marker-assisted breeding for plant type improvement and high-yield potential in rice.     

Association mapping of agronomic traits on chromosome 2A of wheat

Association mapping is a method to test the association between molecular markers and quantitative trait loci (QTL) based on linkage disequilibrium (LD). In this study, the collection of 108 wheat germplasm accessions form China were evaluated for their plant heights, spike length, spikelets per spike, grains per spike, thousand kernel weight and spikelets density in 3 years at three locations. And they were genotyped with 85 SSR markers and 40 EST-SSR markers. The population structure was inferred on the basis of unlinked 48 SSR markers and 40 EST-SSR markers. The extent of LD on chromosome 2A was 2.3 cM. Association of 37 SSR loci on chromosomes 2A with six agronomic traits was analysed with a mixed linear model. A total of 14 SSR loci were significantly associated with agronomic traits. Some of the associated markers were located in the QTL region detected in previous linkage mapping analysis. Our results demonstrated that association mapping can enhance QTL information and achieves higher resolution with short LD extent.     

Association mapping of yield and its components in rice cultivars

To make advances in rice breeding it is important to understand the relatedness and ancestry of introduced rice accessions, and identify SSR markers associated with agronomically important phenotypic traits, for example yield. Ninety-two rice germplasm accessions recently introduced from seven geographic regions of Africa, Asia, and Latin America, and eleven US cultivars, included as checks, were evaluated for yield and kernel characteristics, and genotyped with 123 SSR markers. The SSR markers were highly polymorphic across all accessions. Population structure analysis identified eight main clusters for the accessions which corresponded to the major geographic regions, indicating agreement between genetic and predefined populations. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping association. LD between linked markers decreased with distance and with a substantial drop in LD decay values between 20 and 30 cM, suggesting it should be possible to achieve resolution down to the 25 cM level. For the 103 cultivars, the complex traits yield, kernel width, kernel length, kernel width/length ratio, and 1000-kernel weight, were estimated by analysis of variety trial data. The mixed linear model method was used to disclose marker-trait associations. Many of the associated markers were located in regions where QTL had previously been identified. In conclusion, association mapping in rice is a viable alternative to QTL mapping based on crosses between different lines.     

Quantitative trait loci for grain quality, productivity, morphological and agronomical traits in sorghum (Sorghum bicolor L. Moench)

 Quantitative trait loci (QTLs) for grain quality, yield components and other traits were investigated in two Sorghum caudatum×guinea recombinant inbred line (RIL) populations. A total of 16 traits were evaluated (plant height, panicle length, panicle compactness, number of kernels/panicle, thousand-kernel weight, kernel weight/panicle, threshing percentage, dehulling yield, kernel flouriness, kernel friability, kernel hardness, amylose content, protein content, lipid content, germination rate and molds during germination and after harvest) and related to two 113- and 100-point base genetic maps using simple (SIM) and composite (CIM) interval mapping. The number, effects and relative position of QTLs detected in both populations were generally in agreement with the distributions, heritabilities and correlations among traits. Several chromosomal segments markedly affected multiple traits and were suspected of harbouring major genes. The positions of these QTLs are discussed in relation to previously reported studies on sorghum and other grasses. Many QTLs, depending on their relative effects and position, could be used as targets for marker-assisted selection and provide an opportunity for accelerating breeding programmes. Received: 14 February 1998 / Accepted: 4 March 1998     

Morphological and molecular characterization of new plant type core set for yield and culm strength traits in rice (Oryza sativa L.)

New plant type core set comprising indica and tropical japonica accessions along with checks were evaluated for yield and culm strength related traits and characterized with gene specific markers viz., Gn1a, DEP1, Ghd7, SPL14, GS5, TGW6 and SCM2. Analysis of variance revealed significant differences as well as presence of variability among the genotypes for all the traits. Seven genotypes (IRGC25510, IRGC1742, Haorei machang, Azhoghi, Thangmoi, BPT5204 and Swarnadhan) do not possess similar allele as that of the assessed genes based on combined analysis for all the traits and genes. Of them, four genotypes IRGC1742, Azhoghi, BPT5204 and Swarnadhan possess ideal trait combination (90–100 days to 50% flowering, 100–120 cm plant height, grain number of > 200, 11–15 productive tillers) but with weak culm can be ideal sources for identification of new genes for yield attributing traits and direct introgression of SCM2. Based on single trait-gene analysis, nine trait wise donors with high value for the trait (also with desirable plant type) but without similar allele of the corresponding gene were identified. One genotype IRGC7486 with high grain number (300), four genotypes (IRGC50448, IRGC43741, IRGC15147 and IRGC39111) with strong culm (1195–2655 g.f), three genotypes viz., IRGC15147, IRGC39111 and IRGC10658 with high panicle weight and one genotype Solumpiket with high 1000-grain weight and high panicle weight can be considered for identification of novel gene(s) for respective traits.

     

水稻轮回选择群体XTBG-HP1表型遗传多样性分析

该研究基于4个陆稻群体及172个水稻品种或杂交组合,构建了水稻多亲本隐性核不育轮回选择群体XTBG-HP1,并经过4次轮回重组,采用16个表型性状对其进行了遗传多样性分析。结果表明:(1)该群体14个数量性状符合正态分布,各表型均存在极端性状个体。(2)数量性状变异系数范围为0.08～0.41,均值为0.20; Shannon-Wiener多样性指数范围为0.72～1.92,均值为1.50。(3)群体在株型与产量构成因子性状方面有显著的相关性,对株型的选择可以实现产量性状的改良。(4)剑叶长、每穗粒总数、千粒重、穗长、粒长、一次枝梗数、有效穗数、剑叶宽、二次枝梗数、抽穗期10个性状可作为群体综合评价指标。(5)剑叶长、二次枝梗数、每穗粒总数3个表型性状具有较高的遗传变异、丰富的遗传多样性及与综合得分F值相关系数较高。综合以上结果发现,后期群体进行基因挖掘、品种改良以及优良育种材料的选育可以基于剑叶长、二次枝梗数及每穗粒总数3个表型性状,同时要充分利用群体株型与产量构成因子性状间的显著相关性。此外,该研究群体中极端单性状或综合得分F值较高的个体,可进一步用于品种选育。     

Genetic diversity and population structure of a diverse set of rice germplasm for association mapping

Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25–50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker–trait association mapping. This new association population has the potential to identify quantitative trait loci (QTL) with small effects, which will aid in dissecting complex traits and in exploiting the rich diversity present in rice germplasm.     

Fine Mapping QTL for Drought Resistance Traits in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) Using Bulk Segregant Analysis

Drought stress is a major limitation to rice (Oryza sativa L.) yields and its stability, especially in rainfed conditions. Developing rice cultivars with inherent capacity to withstand drought stress would improve rainfed rice production. Mapping quantitative trait loci (QTLs) linked to drought resistance traits will help to develop rice cultivars suitable for water-limited environments through molecular marker-assisted selection (MAS) strategy. However, QTL mapping is usually carried out by genotyping large number of progenies, which is labour-intensive, time-consuming and cost-ineffective. Bulk segregant analysis (BSA) serves as an affordable strategy for mapping large effect QTLs by genotyping only the extreme phenotypes instead of the entire mapping population. We have previously mapped a QTL linked to leaf rolling and leaf drying in recombinant inbred (RI) lines derived from two locally adapted indica rice ecotypes viz., IR20/Nootripathu using BSA. Fine mapping the QTL will facilitate its application in MAS. BSA was done by bulking DNA of 10 drought-resistant and 12 drought-sensitive RI lines. Out of 343 rice microsatellites markers genotyped, RM8085 co-segregated among the RI lines constituting the respective bulks. RM8085 was mapped in the middle of the QTL region on chromosome 1 previously identified in these RI lines thus reducing the QTL interval from 7.9 to 3.8 cM. Further, the study showed that the region, RM212–RM302–RM8085–RM3825 on chromosome 1, harbours large effect QTLs for drought-resistance traits across several genetic backgrounds in rice. Thus, the QTL may be useful for drought resistance improvement in rice through MAS and map-based cloning.     

Whole-Genome Quantitative Trait Locus Mapping Reveals Major Role of Epistasis on Yield of Rice

Although rice yield has been doubled in most parts of the world since 1960s, thanks to the advancements in breeding technologies, the biological mechanisms controlling yield are largely unknown. To understand the genetic basis of rice yield, a number of quantitative trait locus (QTL) mapping studies have been carried out, but whole-genome QTL mapping incorporating all interaction effects is still lacking. In this paper, we exploited whole-genome markers of an immortalized F₂ population derived from an elite rice hybrid to perform QTL mapping for rice yield characterized by yield per plant and three yield component traits. Our QTL model includes additive and dominance main effects of 1,619 markers and all pair-wise interactions, with a total of more than 5 million possible effects. The QTL mapping identified 54, 5, 28 and 4 significant effects involving 103, 9, 52 and 7 QTLs for the four traits, namely the number of panicles per plant, the number of grains per panicle, grain weight, and yield per plant. Most identified QTLs are involved in digenic interactions. An extensive literature survey of experimentally characterized genes related to crop yield shows that 19 of 54 effects, 4 of 5 effects, 12 of 28 effects and 2 of 4 effects for the four traits, respectively, involve at least one QTL that locates within 2 cM distance to at least one yield-related gene. This study not only reveals the major role of epistasis influencing rice yield, but also provides a set of candidate genetic loci for further experimental investigation.     

Studies on some genetic parameters of rice (Oryza sativa L.)

Summary In order to utilize the available useful variation in breeding rice to improve yield and quality of grain, the performance of a wide range of rice germ plasm comprising 30 varieties was evaluated in northern India, a major rice growing belt. Plant performance revealed high genetic divergence and phenotypic variability in the crop, with the maximum range of variation being for grain number per panicle and the minimum for grain dimensions. There were also significant differences among varietal means for ten phenotypic traits. Genotypic and phenotypic variance contributed profoundly to the variance of the phenotypic traits studied, but, since genetic variability in the traits related to yield was considerable, there is scope for further improvement in yielding ability. Grain number per panicle, number of effective tillers per plant and culm length exhibit high heritability, and genotypic coefficient of variation and therefore a high genetic advance. Thus, selection for these traits would be effective in crop improvement. Moreover, grain number per panicle shows a significant positive correlation with yield, and this trait could profitably form a reliable index for the yielding capacity of this crop.     

两种供氮水平下水稻生长后期相关性状的QTL定位

以特青为母本与Lemont杂交,然后用特青为轮回亲本回交,建立特青背景下的染色体片段置换系（CSSL）群体。在正常和低氮条件下分别在生长后期对株高（PH）、单株穗数（PN）、叶绿素含量（CC）、地上部干物重（SDW）和单株籽粒产量（YD）等性状进行了QTL分析,共检测到31个QTL。其中在正常供氮水平下控制PH、PN、CC、SDW和YD的QTL数目均为3个;在低氮水平下检测到5、4、5和2个影响PH、PN、CC和SDW的QTL,在低氮水平下没有检测到控制YD的位点。大部分QTL集中在第2、3、7、11和12染色体上,影响不同性状或在两种供氮水平下影响同一性状的QTL在染色体上成串或成簇分布。其中RM30-RM439、RM18-RM478、RM309-RM270、RM235-RM17等区域同时检测到控制两个以上性状的QTL,表现出明显的一因多效现象。推测仅在低氮水平下检测到的QTL可能跟水稻对低氮胁迫耐性有一定的关联。