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Heterosis contributes greatly to crop production, but the genetic basis of heterosis is not fully understood. To identify heterotic loci (HLs) for grain yield, 12 yield traits were evaluated in four rice (Oryza sativa L.) mapping populations: one parental population of chromosome segment substitution lines derived from a cross between the japonica cultivar Nipponbare and indica cultivar 9311 and three connected test populations in either a homozygous 9311 genetic background or a heterozygous background. A total of 390 HLs were detected for the measured traits in two environments. The genetic bases of heterosis differed between the backcross and testcross populations. At least 10 HLs were confirmed in F1 hybrids between 9311 and near-isogenic lines, each of which carried a heterotic locus of interest in the same 9311 background. All 10 showed overdominant or dominant effects on grain yield and yield components. Among them, three were verified as being associated with yield heterosis and colocalized in the same regions as those containing previously reported heterosis-associated genes. Five HLs were identified to be promising candidate loci that could be used to achieve more than 15% yield heterosis in several commercial rice hybrids. These findings suggest the potential of indica or japonica introgression for increasing yield in hybrid rice breeding programs. [ABSTRACT FROM AUTHOR]

Grain size is the major determinant of grain weight and has an important role in grain quality. It is controlled by several major quantitative trait loci (QTL) and many minor QTL. Identification of QTL for grain size is important for understanding the genetic and molecular network regulating grain size in rice (Oryza sativa L.). Following previous identification of QTL for grain weight and size using an F2:3 family derived from the indica rice cross Teqing/IRBB52, one QTL, qTGW5, having significant effects on grain length and weight, was targeted for validation, dissection, and fine-mapping. First, the effect of qTGW5 was validated using two near-isogenic line (NIL)-F2 populations. Then, qTGW5 was dissected into two closely linked QTL using four NIL populations. One of them, qGL5.1, having significant effects on grain length, width, and weight, was located within an 1,896.4-kb region. The other one, qGL5.2, controlling grain length, was further delimited into a 68.8-kb region using seven NIL-F2 populations. Six annotated genes were found in the qGL5.2 region, of which five showed nucleotide polymorphisms between the two parental lines. Three of the six annotated genes showed significant expression differences between NILTeqing and NILIRBB52 in young panicles using quantitative real-time polymerase chain reaction. The results will facilitate cloning the minor QTL and understanding the genetic architecture for grain size in rice. [ABSTRACT FROM AUTHOR]

Dissecting the genetic mechanisms underlying agronomic traits is of great importance for crop breeding. Agronomic traits are usually controlled by multiple quantitative trait loci (QTLs) and genetic interactions, and mapping the underlying causal genes is still labor-intensive and time-consuming. Here, we present a genetic tool for directly targeting the specific causal genes by using a single-gene resolution linkage map that was constructed from 3756 F2 rice plants via targeted sequencing technology and Tukey-Kramer multiple comparisons test. Three large- and moderate-effect QTLs, qHD6-2, qGL3-1, and qGW5-2, were successfully mapped to their specific causal genes, Hd1, GS3, and GW5, respectively. A complex genetic interaction network containing 30 QTL–QTL interactions was constructed, revealing that the alternative allele of hub QTL, qHD6-2, can hide or release the genetic contributions of the alleles at interacting loci. Moreover, arranging genetic interactions in the models lead to more accurate phenotypic predictions. These results provide a community resource and new feasible strategy for deciphering the genetic mechanisms of complex agronomic traits and accelerating crop breeding. [ABSTRACT FROM AUTHOR]

Seed storability largely determines the vigor of seeds during storage and is significant in agriculture and ecology. However, the underlying genetic basis remains unclear. In the present study, we report the cloning and characterization of the rice (Oryza sativa) indole-3-acetic acid (IAA)-amido synthetase gene GRETCHEN HAGEN3-2 (OsGH3-2) associated with seed storability. OsGH3-2 was identified by performing a genome-wide association study in rice germplasms with linkage mapping in chromosome substitution segment lines, contributing to the wide variation of seed viability in the populations after long periods of storage and artificial ageing. OsGH3-2 was dominantly expressed in the developing seeds and catalyzed IAA conjugation to amino acids, forming inactive auxin. Transgenic overexpression, knockout, and knockdown experiments demonstrated that OsGH3-2 affected seed storability by regulating the accumulation level of abscisic acid (ABA). Overexpression of OsGH3-2 significantly decreased seed storability, while knockout or knockdown of the gene enhanced seed storability compared with the wild-type. OsGH3-2 acted as a negative regulator of seed storability by modulating many genes related to the ABA pathway and probably subsequently late embryogenesis-abundant proteins at the transcription level. These findings shed light on the molecular mechanisms underlying seed storability and will facilitate the improvement of seed vigor by genomic breeding and gene-editing approaches in rice. [ABSTRACT FROM AUTHOR]

Metabolomic analysis coupled with advanced genetic populations represents a powerful tool with which to investigate the plant metabolome. However, genetic analyses of the rice (Oryza sativa) metabolome have been conducted mainly using natural accessions or a single biparental population. Here, the flag leaves from three interconnected chromosome segment substitution line populations with a common recurrent genetic background were used to dissect rice metabolic diversity. We effectively used multiple interconnected biparental populations, constructed by introducing genomic segments into Zhenshan 97 from ACC10 (A/Z), Minghui 63 (M/Z), and Nipponbare (N/Z), to map metabolic quantitative trait loci (mQTL). A total of 1,587 mQTL were generated, of which 684, 479, and 722 were obtained from the A/Z, M/Z, and N/Z chromosome segment substitution line populations, respectively, and we designated 99 candidate genes for 367 mQTL. In addition, 1,001 mQTL were generated specifically from joint linkage analysis with 25 candidate genes assigned. Several of these candidates were validated, such as LOC_Os07g01020 for the in vivo content of pyridoxine and its derivative and LOC_Os04g25980 for cis-zeatin glucosyltransferase activity. We propose a novel biosynthetic pathway for O-methylapigenin C-pentoside and demonstrated that LOC_Os04g11970 encodes a component of this pathway through fine-mapping. We postulate that the methylated apigenin may confer plant disease resistance. This study demonstrates the power of using multiple interconnected populations to generate a large number of veritable mQTL. The combined results are discussed in the context of functional metabolomics and the possible features of assigned candidates underlying respective metabolites. [ABSTRACT FROM AUTHOR]

Background: Mechanized dry seeded rice can save both labour and water resources. Rice seedling establishment is sensitive to sowing depth while mesocotyl elongation facilitates the emergence of deeply sown seeds. Results: A set of 270 rice accessions, including 170 from the mini-core collection of Chinese rice germplasm (C Collection) and 100 varieties used in a breeding program for drought resistance (D Collection), was screened for mesocotyl lengths of seedlings grown in water (MLw) in darkness and in 5 cm sand culture (MLs). Twenty six accessions (10.53 %) have MLw longer than 1.0 cm. Eleven accessions had the highest mesocotyl lengths, i.e. 1.4 - 5.05 cm of MLw and 3.0 - 6.4 cm in 10 cm sand culture, including 7 upland landraces or varieties. The genotypic data of 1,019,883 SNPs were developed by re-sequencing of those accessions. A wholegenome SNP array (Rice SNP50) was used to genotype 24 accessions as a validation panel, giving 98.41 % of consistent SNPs with the re-sequencing data in average. GWAS based on compressed mixed linear model was conducted using GAPIT. Based on a threshold of - log(P) ≥8.0, 13 loci were associated to MLw on rice chromosome 1, 3, 4, 5, 6 and 9, respectively. Three associated loci, on chromosome 3, 6, and 10, were detected for MLs. A set of 99 associated SNPs for MLw, based on a compromised threshold (-log(P) ≥7.0), located in intergenic regions or different positions of 36 annotated genes, including one cullin and one growth regulating factor gene. Conclusions: Higher proportion and extension of elongated mesocotyls were observed in the mini-core collection of rice germplasm and upland rice landraces or varieties, possibly causing the correlation between mesocotyl elongation and drought resistance. GWAS found 13 loci for mesocotyl length measured in dark germination that confirmed the previously reported co-location of two QTLs across populations and experiments. Associated SNPs hit 36 annotated genes including function-matching candidates like cullin and GRF. The germplasm with elongated mesocotyl, especially upland landraces or varieties, and the associated SNPs could be useful in further studies and breeding of mechanized dry seeded rice. [ABSTRACT FROM AUTHOR]

Plantmetabolites are crucial for both plant life and human nutrition. Despite recent advance in metabolomics, the genetic control of plant metabolome remains largely unknown. Here, we performed a genetic analysis of the rice metabolome that provided over 2,800 highly resolved metabolic quantitative trait loci for 900 metabolites. Distinct and overlapping accumulation patterns of metabolites were observed and complex genetic regulation of metabolism was revealed in two different tissues. We associated 24 candidate genes to various metabolic quantitative trait loci by data mining, including ones regulating important morphological traits and biological processes. The corresponding pathways were reconstructed by updating in vivo functions of previously identified and newly assigned genes. This study demonstrated a powerful tool and provided a vast amount of high-quality data for understanding the plasticity of plant metabolome, which may help bridge the gap between the genome and phenome. [ABSTRACT FROM AUTHOR]

Background: Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. Methodology/Principal Findings: In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. Conclusions/Significance: The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1-6 in this study) were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability. [ABSTRACT FROM AUTHOR]

Background: Ammonium is one of the major forms in which nitrogen is available for plant growth. OsAMT1;1 is a high-affinity ammonium transporter in rice (Oryza sativa L.), responsible for ammonium uptake at low nitrogen concentration. The expression pattern of the gene has been reported. However, variations in its nucleotides and the evolutionary pathway of its descent from wild progenitors are yet to be elucidated. In this study, nucleotide diversity of the gene OsAMT1;1 and the diversity pattern of seven gene fragments spanning a genomic region approximately 150 kb long surrounding the gene were surveyed by sequencing a panel of 216 rice accessions including both cultivated rice and wild relatives. Results: Nucleotide polymorphism (Pi) of OsAMT1;1 was as low as 0.00004 in cultivated rice (Oryza sativa), only 2.3% of that in the common wild rice (O. rufipogon). A single dominant haplotype was fixed at the locus in O. sativa. The test values for neutrality were significantly negative in the entire region stretching 5' upstream and 3' downstream of the gene in all accessions. The value of linkage disequilibrium remained high across a 100 kb genomic region around OsAMT1;1 in O. sativa, but fell rapidly in O. rufipogon on either side of the promoter of OsAMT1;1, demonstrating a strong natural selection within or nearby the ammonium transporter. Conclusions: The severe reduction in nucleotide variation at OsAMT1;1 in rice was caused by a selective sweep around OsAMT1;1, which may reflect the nitrogen uptake system under strong selection by the paddy soil during the domestication of rice. Purifying selection also occurred before the wild rice diverged into its two subspecies, namely indica and japonica. These findings would provide useful insights into the processes of evolution and domestication of nitrogen uptake genes in rice. [ABSTRACT FROM AUTHOR]

Grain yield in many cereal crops is largely determined by grain size. Here we report the genetic and molecular characterization of G53, a major quantitative trait locus for grain size. It functions as a negative regulator of grain size and organ size. The wild-type isoform is composed of four putative domains: a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane do- main. a tumor necrosis factor receptor/nerve growth factor recep- tor (TNFR/NGFR) family cysteine-rich domain, and a von Willebrand factor type C (VWFC) in the C terminus. These domains function differentially in grain size regulation. The OSR domain is both necessary and sufficient for functioning as a negative regulator. The wild-type allele corresponds to medium grain. Loss of function of OSR results in long grain. The C-terminal TNFR/NGFR and VWFC domains show an inhibitory effect on the OSR function: loss-of- function mutations of these domains produced very short grain. This study linked the functional domains of the GS3 protein to natural variation of grain size in rice. [ABSTRACT FROM AUTHOR]

Analyses of quantitative trait loci (QTLs) for expression levels (eQTLs) of genes reveal a genetic relationship between expression variation and the regulator, thus unlocking information for identifying the regulatory network. Oligo-nucleotide expression microarrays hybridized with RNA can simultaneously provide data for molecular markers and transcript abundance. In this study, we used an Affymetrix GeneChip Rice Genome Array to analyze eQTLs in rice shoots at 72 h after germination from 110 recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63. In total, 1632 single-feature polymorphisms (SFPs) plus 23 PCR markers were identified and placed into 601 recombinant bins, spanning 1459 cM in length, which were used as markers to genotype the RILs. We obtained 16 372 expression traits (e-traits) each with at least one eQTL, resulting in 26 051 eQTLs in total, including both cis- and trans-eQTLs. We also identified 171 eQTL hot spots in the rice genome, each of which controls transcript variations of many e-traits. Gene ontology analysis revealed an enrichment of certain functional categories of genes in some of the eQTL hot spots. In particular, eQTLs for e-traits involving the DNA metabolic process was significantly enriched in several eQTL hot spots on chromosomes 3, 5 and 10. Several e-traits co-localizing with cis-eQTLs showed significant correlations with hundreds of e-traits, indicating possible co-regulation. We also detected correlations between QTLs for shoot dry weight and eQTLs, revealing possible candidate genes for the trait. These results provided clues for the identification and characterization of the regulatory network in the whole genome at the transcriptional level. [ABSTRACT FROM AUTHOR]

Bar-coded multiplexed sequencing approaches based on newgeneration 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 0.05x 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 (GWS) 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. [ABSTRACT FROM AUTHOR]

The majority of 170 rice accessions used in this study were diverse landraces or varieties from a putative mini-core collection of Chinese germplasm along with some widely used parental lines in genetic analysis or breeding (a few from abroad). The population was genotyped using 84 SSR or InDel markers on chromosome 7 and 48 markers on other chromosomes. The phenotyping of heading date, plant height and panicle length were carried out in different locations for 2 years. Based on morphological characterization, distance-based clustering and model-based estimation of marker data, the population showed a predominant structure with two subpopulations in correspondence with indica and japonica subspecies. The estimation of linkage disequilibrium in 2 Mb windows varied along chromosome 7 and showed parallel changes with inter-subspecies differentiation of marker loci ( Fst). Based on the mixed linear model considering population structure and family relatedness [i.e. the ( Q + K) model], one to three associated markers ( P ≤ 0.0001) per trait per experiment were scanned out on rice chromosome 7. Most significant loci were repeated for the data from both field experiments while two loci were associated with two or three traits. Marker-based allelic effects were shown in a couple of associated markers as examples. The application of association results in breeding program was also discussed. [ABSTRACT FROM AUTHOR]

Abstract  The genetic transformation efficiency of a rice variety is largely determined by its tissue culturability. Establishment of a highly efficient tissue-culture system has greatly accelerated the wide spread application of transgenic japonica varieties. However, such process for indica rice was hampered because this type of variety is recalcitrant to in vitro culture. This study aimed to map the quantitative trait loci (QTLs) for mature seed culturability using a chromosomal segment substitution lines (CSSL) population derived from a cross between an indica variety “Zhenshan 97B” and a japonica variety “Nipponbare”. The CSSLs consist of 139 lines each containing a single or a few introgression segments, and together covering the whole “Nipponbare” genome. Every CSSL was tested by culturing on the two medium systems developed for the respective indica and japonica parental varieties. The performance of culturability was evaluated by four indices: frequency of callus induction (CIF), callus subculture capability (CSC), frequency of plant regeneration (PRF) and the mean plantlet number per regenerated callus (MNR). All four traits displayed continuous variation among the CSSLs. With the culture system for japonica rice, three CIF QTLs, three CSC QTLs, three PRF QTLs and three MNR QTLs were detected. With the culture system for indica variety, six CIF QTLs, two CSC QTLs, three PRF QTLs and six MNR QTLs were identified, and these QTLs distributed on nine rice chromosomes. Two QTLs of CIF and two QTLs of MNR were detected in both the japonica and indica rice culture system. The correlation coefficients of all the four traits varied depending on the culture systems. These results provide the possibilities of enhancing the culturability of indica rice by marker-assisted breeding with those desirable alleles from the japonica. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

A greater understanding of the genetics of responses to water deficit/drought may be helpful in improving water-deficit resistance in the early stages of growth in rice. A recombinant inbred population derived from a cross between Zhenshan 97 and Minghui 63 was grown in hydroponic culture to characterize the responses of seedlings to water deficit imposed by PEG 6000 and to identify quantitative trait loci (QTLs) for seedling characteristics under both well-watered and water-deficit conditions. Generally, the two parents showed significant differences in plant height (PH), maximum root length (MRL), shoot fresh weight (SFW), root fresh weight (RFW), number of roots and root:shoot ratio based on fresh weight under both well-watered and water-deficit conditions. For two parents, PH and SFW were significantly inhibited under water deficit. However, the other four traits had larger values under water deficit. Among 26 and 34 QTLs detected for the six traits studied under the well-watered and water-deficit conditions, respectively, a total of 14 QTLs for SFW, PH, RFW and MRL (23% of total QTLs detected) were detected in similar or tight linkage regions in both conditions. Among 11 intervals on 7 chromosomes identified to harbor multiple QTLs, 8 intervals were found to affect related traits under the two water supply conditions and 3 intervals were observed to be water supply-specific regions and had effects only under well-watered conditions, suggesting that water supply-specific regions or QTLs may be closely associated with the responses of lines to water deficit in the study. Several regions for the traits studied were also found to affect the root-related traits in previous studies and might be used in marker-assisted selection for drought-resistant rice in breeding programs. [ABSTRACT FROM AUTHOR]

The genetic basis of heterosis of an elite rice hybrid was investigated by using an "immortalized F[sub 2]" 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 F[sub 2] 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 F[sub 2] 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. [ABSTRACT FROM AUTHOR]