Yongzhong Xing

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice

Yield potential, plant height and heading date are three classes of traits that determine the productivity of many crop plants. Here we show that the quantitative trait locus (QTL) Ghd7, isolated from an elite rice hybrid and encoding a CCT domain protein, has major effects on an array of traits in rice, including number of grains per panicle, plant height and heading date. Enhanced expression of Ghd7 under long-day conditions delays heading and increases plant height and panicle size. Natural mutants with reduced function enable rice to be cultivated in temperate and cooler regions. Thus, Ghd7 has played crucial roles for increasing productivity and adaptability of rice globally.

Natural variation in GS5 plays an important role in regulating grain size and yield in rice

Increasing crop yield is one of the most important goals of plant science research. Grain size is a major determinant of grain yield in cereals and is a target trait for both domestication and artificial breeding. We showed that the quantitative trait locus (QTL) GS5 in rice controls grain size by regulating grain width, filling and weight. GS5 encodes a putative serine carboxypeptidase and functions as a positive regulator of grain size, such that higher expression of GS5 is correlated with larger grain size. Sequencing of the promoter region in 51 rice accessions from a wide geographic range identified three haplotypes that seem to be associated with grain width. The results suggest that natural variation in GS5 contributes to grain size diversity in rice and may be useful in improving yield in rice and, potentially, other crops.

Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice

Abstract.Main effects, epistatic effects and their environmental interactions of QTLs are all important genetic components of quantitative traits. In this study, we analyzed the main effects, epistatic effects of the QTLs, and QTL by environment interactions (QEs) underlying four yield traits, using a population of 240 recombinant inbred lines from a cross between two rice varieties tested in replicated field trials. A genetic linkage map with 220 DNA marker loci was constructed. A mixed linear model approach was used to detect QTLs with main effects, QTLs involved in digenic interactions and QEs. In total, 29 QTLs of main effects, and 35 digenic interactions involving 58 loci were detected for the four traits. Thirteen QTLs with main effects showed QEs; no QE was detected for the QTLs involved in epistatic interactions. The amount of variations explained by the QTLs of main effect were larger than the QTLs involved in epistatic interactions, which in turn were larger than QEs for all four traits. This study illustrates the ability of the analysis to assess the genetic components underlying the quantitative traits, and demonstrates the relative importance of the various components as the genetic basis of yield traits in this population.

Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid

The genetic basis of heterosis of an elite rice hybrid was investigated by using an “immortalized F2” population produced by randomly permutated intermating of 240 recombinant inbred lines from a cross between the parents of Shanyou 63, the most widely cultivated hybrid in China. Measurements of heterosis for crosses in the immortalized F2 population were obtained from replicated field trials over 2 years by inter-planting the hybrids with the parental recombinant inbred lines. The analyses were conducted making use of a linkage map comprising 231 segregating molecular marker loci covering the entire rice genome. Heterotic effects were detected at 33 loci for the four traits with modified composite interval mapping. The heterotic loci showed little overlap with quantitative trait loci for trait performance, suggesting that heterosis and trait performance may be conditioned by different sets of loci. Large numbers of digenic interactions were resolved by using two-way ANOVA and confirmed by randomization tests. All kinds of genetic effects, including partial-, full-, and overdominance at single-locus level and all three forms of digenic interactions (additive by additive, additive by dominance, and dominance by dominance), contributed to heterosis in the immortalized F2 population, indicating that these genetic components were not mutually exclusive in the genetic basis of heterosis. Heterotic effects at the single-locus level, in combination with the marginal advantages of double heterozygotes caused by dominance by dominance interaction at the two-locus level could adequately explain the genetic basis of heterosis in Shanyou 63. These results may help reconcile the century-long debate concerning the genetic basis of heterosis.

Genetic Basis of Drought Resistance at Reproductive Stage in Rice: Separation of Drought Tolerance From Drought Avoidance

Drought tolerance (DT) and drought avoidance (DA) are two major mechanisms in drought resistance of higher plants. In this study, the genetic bases of DT and DA at reproductive stage in rice were analyzed using a recombinant inbred line population from a cross between an indica lowland and a tropical japonica upland cultivar. The plants were grown individually in PVC pipes and two cycles of drought stress were applied to individual plants with unstressed plants as the control. A total of 21 traits measuring fitness, yield, and the root system were investigated. Little correlation of relative yield traits with potential yield, plant size, and root traits was detected, suggesting that DT and DA were well separated in the experiment. A genetic linkage map consisting of 245 SSR markers was constructed for mapping QTL for these traits. A total of 27 QTL were resolved for 7 traits of relative performance of fitness and yield, 36 QTL for 5 root traits under control, and 38 for 7 root traits under drought stress conditions, suggesting the complexity of the genetic bases of both DT and DA. Only a small portion of QTL for fitness- and yield-related traits overlapped with QTL for root traits, indicating that DT and DA had distinct genetic bases.

A Major QTL, Ghd8, Plays Pleiotropic Roles in Regulating Grain Productivity, Plant Height, and Heading Date in Rice

Rice yield and heading date are two distinct traits controlled by quantitative trait loci (QTLs). The dissection of molecular mechanisms underlying rice yield traits is important for developing high-yielding rice varieties. Here, we report the cloning and characterization of Ghd8, a major QTL with pleiotropic effects on grain yield, heading date, and plant height. Two sets of near isogenic line populations were developed for the cloning of Ghd8. Ghd8 was narrowed down to a 20-kb region containing two putative genes, of which one encodes the OsHAP3 subunit of a CCAAT-box binding protein (HAP complex); this gene was regarded as the Ghd8 candidate. A complementary test confirmed the identity and pleiotropic effects of the gene; interestingly, the genetic effect of Ghd8 was dependent on its genetic background. By regulating Ehd1, RFT1, and Hd3a, Ghd8 delayed flowering under long-day conditions, but promoted flowering under short-day conditions. Ghd8 up-regulated MOC1, a key gene controlling tillering and branching; this increased the number of tillers, primary and secondary branches, thus producing 50% more grains per plant. The ectopic expression of Ghd8 in Arabidopsis caused early flowering by 10 d-a situation similar to the one observed by its homolog AtHAP3b, when compared to wild-type under long-day conditions; these findings indicate the conserved function of Ghd8 and AtHAP3b in flowering in Arabidopsis. Our results demonstrated the important roles of Ghd8 in rice yield formation and flowering, as well as its opposite functions in flowering between rice and Arabidopsis under long-day conditions.

The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63.

Abstract The cooking and eating quality of the rice grain is one of the most serious problems in many rice-producing areas of the world. In this study, we conducted a molecular marker-based genetic analysis of three traits, amylose content (AC), gel consistency (GC) and gelatinization temperature (GT), that are the most important constituents of the cooking and eating quality of rice grains. The materials used in the analysis included F2 seeds, an F2:3 population, and an F9 recombinant inbred-line population from a cross between the parents of ’Shanyou 63’, the most widely grown hybrid in rice production in China. Segregation analyses of these three generations showed that each of the three traits was controlled by a single Mendelian locus. Molecular marker-based QTL (quantitative trait locus) analyses, both by one-way analysis of variance using single marker genotypes and by whole-genome scanning with MAPMAKER/QTL, revealed a single locus that controls the expression of all three traits. This locus coincided with the Wx region on the short arm of chromosome 6, indicating that all three traits were either controlled by the Wx locus or by a genomic region tightly linked to this locus. This finding has provided clues to resolving the molecular bases of GC and GT in future studies. The results also have direct implications for the quality improvement of rice varieties.

Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid

Abstract Appearance quality of the rice grain represents a major problem of rice production in many rice-producing areas of the world, especially in hybrid rice production in China. In this study, we conducted a molecular marker-based genetic analysis of the traits that are determinants of the appearance quality of rice grains, including traits specifying grain shape and endosperm opacity. The materials used in the analysis included an F2:3 population and an F10 recombinant inbred line population from a cross between the parents of Shanyou 63, the most widely grown rice hybrid in China. Molecular marker-based QTL (quantitative trait locus) analyses revealed that grain length and grain width were each controlled by a major QTL accounting for a very large proportion of the genetic variation, plus one or two minor QTLs each explaining a small proportion of the genetic variation. The major QTLs can be detected in both the F2:3 and recombinant inbred line population using both paddy rice and brown rice, whereas the minor QTLs were detected only occasionally. The QTL located in the interval of RG393-C1087 on chromosome 3 is the major locus for grain length, and the one in the interval RG360-C734a on chromosome 5 plays a major role in determining grain width. Similarly, white belly, which largely determines the opacity of the endosperm, is almost entirely controlled by a major locus on chromosome 5, located in the same genomic region as the major QTL for grain width. The implications of the results with respect to hybrid rice improvement were discussed.

Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge to genotype individual lines in a population for linkage map construction based on low-coverage sequences without the availability of high-quality genotype data of the parental lines. In this paper, we report a method for constructing ultrahigh-density linkage maps composed of high-quality single-nucleotide polymorphisms (SNPs) based on low-coverage sequences of recombinant inbred lines. First, all potential SNPs were identified to obtain drafts of parental genotypes using a maximum parsimonious inference of recombination, making maximum use of SNP information found in the entire population. Second, high-quality SNPs were identified by filtering out low-quality ones by permutations involving resampling of windows of SNPs followed by Bayesian inference. Third, lines in the mapping population were genotyped using the high-quality SNPs assisted by a hidden Markov model. With 0.05× genome sequence per line, an ultrahigh-density linkage map composed of bins of high-quality SNPs using 238 recombinant inbred lines derived from a cross between two rice varieties was constructed. Using this map, a quantitative trait locus for grain width (GW5) was localized to its presumed genomic region in a bin of 200 kb, confirming the accuracy and quality of the map. This method is generally applicable in genetic map construction with low-coverage sequence data.

Gains in QTL Detection Using an Ultra-High Density SNP Map Based on Population Sequencing Relative to Traditional RFLP/SSR Markers

Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL) analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs), thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs) from low-coverage sequences of a recombinant inbred line (RIL) population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs.