Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.)

QTL mapping and improvement of pre-harvest sprouting resistance using japonica weedy rice

The stability of cultivation and production in terms of crop yield has been threatened by climate change due to global warming. Pre-harvest sprouting (PHS) is a threat to crops, especially staple foods, including rice, because of reductions in yield and quality. To address the problem of precocious germination before harvest, we performed quantitative trait loci (QTL) analysis for PHS using F₈ RILs populations derived from japonica weedy rice in Korea. QTL analysis revealed that two stable QTLs, qPH7 and qPH2, associated with PHS resistance were identified on chromosomes 7 and 2, respectively, explaining approximately 38% of the phenotypic variation. The QTL effect in the tested lines significantly decreased the degree of PHS, based on the number of QTLs included. Through fine mapping for main QTL qPH7, the region for the PHS was found to be anchored within 23.575-23.785 Mbp on chromosome 7 using 13 cleaved amplified sequence (CAPS) markers. Among 15 open reading frames (ORFs) within the detected region, one ORF, Os07g0584366, exhibited upregulated expression in the resistant donor, which was approximately nine times higher than that of susceptible japonica cultivars under PHS-inducing conditions. Japonica lines with QTLs related to PHS resistance were developed to improve the characteristics of PHS and design practical PCR-based DNA markers for marker-assisted backcrosses of many other PHS-susceptible japonica cultivars.

Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice

Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of 195 diverse re-sequenced accessions from 40 countries was evaluated for the seed germination rate (GR) without dormancy breaking (WDB) as a control and under dry heating (DH) and gibberellic acid (GA) treatments, as dormancy breaking agents to identify QTLs for seed dormancy. Phenotypic assessment revealed that these accessions had abundant variations in seed dormancy. GWAS using 1,120,223 high-quality single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM) incorporating both principal components (PCs) and kinship (K) identified 30 QTLs on 10 chromosomes, accounting for 7.3-20.4% of the phenotypic variance in GR. Ten of the QTLs were located in the regions of previously reported QTLs, while the rest were novel ones. Thirteen high-confidence candidate genes were predicted for the four QTLs detected in two or three conditions (qGR4-4, qGR4-5, qGR8 and qGR11-4) and one QTL with a large effect (qGR3). These genes were highly expressed during seed development and were significantly regulated by various hormone treatments. This study provides new insights into the genetic and molecular basis of rice seed dormancy/germination. The accessions with moderate and strong dormancy and markers for the QTLs and candidate genes are useful for attaining a proper level of seed dormancy.

Association study of SNP locus for color related traits in herbaceous peony (Paeonia lactiflora Pall.) using SLAF-seq

Paeonia lactiflora Pall. (P. lactiflora) is a famous ornamental plant with showy and colorful flowers that has been domesticated in China for 4,000 years. However, the genetic basis of phenotypic variation and genealogical relationships in P. lactiflora population is poorly understood due to limited genetic information, which brings about bottlenecks in the application of effective and efficient breeding strategies. Understanding the genetic basis of color-related traits is essential for improving flower color by marker-assisted selection (MAS). In this study, a high throughput sequencing of 99 diploid P. lactiflora accessions via specific-locus amplified fragment sequencing (SLAF-seq) technology was performed. In total, 4,383,645 SLAF tags were developed from 99 P. lactiflora accessions with an average sequencing depth of 20.81 for each SLAF tag. A total of 2,954,574 single nucleotide polymorphisms (SNPs) were identified from all SLAF tags. The population structure and phylogenetic analysis showed that P. lactiflora population used in this study could be divided into six divergent groups. Through association study using Mixed linear model (MLM), we further identified 40 SNPs that were significantly positively associated with petal color. Moreover, a derived cleaved amplified polymorphism (dCAPS) marker that was designed based on the SLAF tag 270512F co-segregated with flower colors in P. lactiflora population. Taken together, our results provide valuable insights into the application of MAS in P. lactiflora breeding programs.

Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

BACKGROUND

Breeding of conventional and hybrid rice (Oryza sativa L.) have solved hunger problems and increased farmers' income in the world. Molecular markers have been widely used in marker-assisted breeding and identification of larger numbers of different bred varieties in the past decades. The recently developed SNP markers are applied for more stable and detectable compared with other markers. But the cost of genotyping lots SNPs is high. So, it is essential to select less representative SNPs and inexpensive detecting methods to lower the cost and accelerate variety identification and breeding process. KASP (Kompetitive Allele-Specific PCR) is a flexible method to detect the SNPs, and large number of KASP markers have been widely used in variety identification and breeding. However, the ability of less KASP markers on massive variety identification and breeding remains unknown.

RESULTS

Here, 48 KASP markers were selected from 378 markers to classify and analyze 518 varieties including conventional and hybrid rice. Through analyzing the population structure, the 48 markers could almost represent the 378 markers. In terms of variety identification, the 48 KASP markers had a 100% discrimination rate in 53 conventional indica varieties and 193 hybrid varieties, while they could distinguish 89.1% conventional japonica rice from different breeding institutes. Two more markers added would increase the ratio from 68.38 to 77.94%. Additionally, the 48 markers could be used for classification of subpopulations in the bred variety. Also, 8 markers had almost completely different genotypes between japonica and indica, and 3 markers were found to be very important for japonica hybrid rice. In hybrid varieties, the heterozygosity of chromosomes 3, 6 and 11 was relatively higher than others.

CONCLUSIONS

Our results showed that 48 KASP markers could be used to identify rice varieties, and the panel we tested could provide a database for breeders to identify new breeding lines. Also, the specific markers we found were useful for marker-assisted breeding in rice, including conventional and hybrid.

Sdr4 dominates pre-harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice

Pre-harvest sprouting (PHS), which reduces grain yield and quality, is controlled by seed dormancy genes. Because few dormancy-related genes have been cloned, the genetic basis of seed dormancy in rice (Oryza sativa L.) remains unclear. Here, we performed a genome-wide association study and linkage mapping to dissect the genetic basis of seed dormancy in rice. Our findings suggest that Seed Dormancy4 (Sdr4), a central modulator of seed dormancy, integrates the abscisic acid and gibberellic acid signaling pathways at the transcriptional level. Haplotype analysis revealed that three Sdr4 alleles in rice cultivars already existed in ancestral Oryza rufipogon accessions. Furthermore, like the semi-dwarf 1 (SD1) and Rc loci, Sdr4 underwent selection during the domestication and improvement of Asian cultivated rice. The distribution frequency of the Sdr4-n allele in different locations in Asia is negatively associated with local annual temperature and precipitation. Finally, we developed functional molecular markers for Sdr4, SD1, and Rc for use in molecular breeding. Our results provide clues about the molecular basis of Sdr4-regulated seed dormancy. Moreover, these findings provide guidance for utilizing the favorable alleles of Sdr4 and Rc to synergistically boost PHS resistance, yield, and quality in modern rice varieties.

Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice

Several QTLs and genes responsible for seed dormancy were detected and SNP candidates were shown to cause changes in seed germination. Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice (Oryza sativa L.), wheat (Triticum aestivum), and barley (Hordeum vulgare L.). However, our knowledge of seed dormancy is hampered by the complexities of studying a trait that changes over time after seed harvest, and is complicated by interactions between phytohormones, seed coat components and the environment. Here, we have conducted a genome-wide association study using a panel of 311 natural accessions of cultivated rice, examining a total of 519,158 single nucleotide polymorphisms (SNPs). Eight quantitative trait loci (QTLs) were found to associate with seed dormancy in the whole panel and five in the Japonica and Indica subpanel; expression of candidate genes within 100 kb of each QTL was examined in two published, germination-specific transcriptomic datasets. Ten candidate genes, differentially expressed within the first four days post-imbibition, were identified. Five of these genes had previously been associated with awn length, heading date, yield, and spikelet length phenotypes. Two candidates were validated using Quantitative Reverse Transcription (qRT)-PCR. In addition, previously identified genes involved in hormone signaling during germination were found to be differentially expressed between a japonica and an indica line; SNPs in the promoter of Os9BGlu33 were associated with germination index, with qRT-PCR validation. Collectively, our results are useful for future characterization of seed dormancy mechanism and crop improvement, and suggest haplotypes for further analysis that may be of use to boost PHS resistance in rice.

Seed Dormancy and Pre-Harvest Sprouting in Rice-An Updated Overview

Pre-harvest sprouting is a critical phenomenon involving the germination of seeds in the mother plant before harvest under relative humid conditions and reduced dormancy. As it results in reduced grain yield and quality, it is a common problem for the farmers who have cultivated the rice and wheat across the globe. Crop yields need to be steadily increased to improve the people’s ability to adapt to risks as the world’s population grows and natural disasters become more frequent. To improve the quality of grain and to avoid pre-harvest sprouting, a clear understanding of the crops should be known with the use of molecular omics approaches. Meanwhile, pre-harvest sprouting is a complicated phenomenon, especially in rice, and physiological, hormonal, and genetic changes should be monitored, which can be modified by high-throughput metabolic engineering techniques. The integration of these data allows the creation of tailored breeding lines suitable for various demands and regions, and it is crucial for increasing the crop yields and economic benefits. In this review, we have provided an overview of seed dormancy and its regulation, the major causes of pre-harvest sprouting, and also unraveled the novel avenues to battle pre-harvest sprouting in cereals with special reference to rice using genomics and transcriptomic approaches.

Molecular dissection of maize seedling salt tolerance using a genome-wide association analysis method

Salt stress is a major devastating abiotic factor that affects the yield and quality of maize. However, knowledge of the molecular mechanisms of the responses to salt stress in maize is limited. To elucidate the genetic basis of salt tolerance traits, a genome-wide association study was performed on 348 maize inbred lines under normal and salt stress conditions using 557 894 single nucleotide polymorphisms (SNPs). The phenotypic data for 27 traits revealed coefficients of variation of >25%. In total, 149 significant SNPs explaining 6.6%-11.2% of the phenotypic variation for each SNP were identified. Of the 104 identified quantitative trait loci (QTLs), 83 were related to salt tolerance and 21 to normal traits. Additionally, 13 QTLs were associated with two to five traits. Eleven and six QTLs controlling salt tolerance traits and normal root growth, respectively, co-localized with QTL intervals reported previously. Based on functional annotations, 13 candidate genes were predicted. Expression levels analysis of 12 candidate genes revealed that they were all responsive to salt stress. The CRISPR/Cas9 technology targeting three sites was applied in maize, and its editing efficiency reached 70%. By comparing the biomass of three CRISPR/Cas9 mutants of ZmCLCg and one zmpmp3 EMS mutant with their wild-type plants under salt stress, the salt tolerance function of candidate genes ZmCLCg and ZmPMP3 were confirmed. Chloride content analysis revealed that ZmCLCg regulated chloride transport under sodium chloride stress. These results help to explain genetic variations in salt tolerance and provide novel loci for generating salt-tolerant maize lines.

Advances in the Identification of Quantitative Trait Loci and Genes Involved in Seed Vigor in Rice

Seed vigor is a complex trait, including the seed germination, seedling emergence, and growth, as well as seed storability and stress tolerance, which is important for direct seeding in rice. Seed vigor is established during seed development, and its level is decreased during seed storage. Seed vigor is influenced by genetic and environmental factors during seed development, storage, and germination stages. A lot of factors, such as nutrient reserves, seed dying, seed dormancy, seed deterioration, stress conditions, and seed treatments, will influence seed vigor during seed development to germination stages. This review highlights the current advances on the identification of quantitative trait loci (QTLs) and regulatory genes involved in seed vigor at seed development, storage, and germination stages in rice. These identified QTLs and regulatory genes will contribute to the improvement of seed vigor by breeding, biotechnological, and treatment approaches.

Genome-wide association study reveals novel genetic loci contributing to cold tolerance at the germination stage in indica rice

Low temperature at the germination stage is one of the major abiotic stresses limiting rice (Oryza sativa L.) production, especially in regions where rice seeds are sown directly. However, few relevant genetic loci and genes have been identified. In this study, we report the phenotypic analysis of low temperature germination (LTG) in 200 indica rice varieties and a genome-wide association study (GWAS) of LTG in this collection using 161,657 high-quality SNPs, which were identified via genotyping-by-sequencing (GBS) of all the rice varieties. A total of 159 genetic loci were detected, and they were evenly distributed on all 12 chromosomes. Among them, 51 loci were detected more than twice; in particular, 23 loci were detected repeatedly in both the wet and dry seasons, and 569 genes were predicted in the 200-kb genomic region harbouring these 23 loci. Furthermore, 14,742 differentially expressed genes (DEGs) were identified using RNA sequencing. By integrating GWAS and RNA sequencing, 179 candidate DEGs were obtained. Sequence variation in the region of loci 95 was analyzed using 20 varieties with extreme phenotype. The polymorphisms of three DEGs (Os07g0585500, Os07g0585700, Os07g0585900) were associated with their phenotypes. Haplotype analysis of the three genes demonstrated that almost all the varieties with the same haplotype as japonica Nipponbare on the three DEGs showed high LTG ability. These findings provide valuable information for understanding the genetic control of LTG and performing molecular breeding with marker-assisted selection in indica rice.

Genetic Dissection of Seed Dormancy in Rice (Oryza sativa L.) by Using Two Mapping Populations Derived from Common Parents

BACKGROUND

Seed dormancy, a quality characteristic that plays a role in seed germination, seedling establishment and grain yield, is affected by multiple genes and environmental factors. The genetic and molecular mechanisms underlying seed dormancy in rice remain largely unknown.

RESULTS

Quantitative trait loci (QTLs) for seed dormancy were identified in two different mapping populations, a chromosome segment substitution line (CSSL) and backcross inbred line (BIL) population, both derived from the same parents Nipponbare, a japonica cultivar with seed dormancy, and 9311, an indica cultivar lacking seed dormancy. A total of 12 and 27 QTL regions for seed dormancy were detected in the CSSLs and BILs, respectively. Among these regions, four major loci (qSD3.1, qSD3.2, qSD5.2 and qSD11.2) were commonly identified for multiple germination parameters associated with seed dormancy in both populations, with Nipponbare alleles delaying the seed germination percentage and decreasing germination uniformity. Two loci (qSD3.1 and qSD3.2) were individually validated in the near-isogenic lines containing the QTL of interest. The effect of qSD3.2 was further confirmed in a CSSL-derived F₂ population. Furthermore, both qSD3.1 and qSD3.2 were sensitive to abscisic acid and exhibited a significant epistatic interaction to increase seed dormancy.

CONCLUSIONS

Our results indicate that the integration of the developed CSSLs and BILs with high-density markers can provide a powerful tool for dissecting the genetic basis of seed dormancy in rice. Our findings regarding the major loci and their interactions with several promising candidate genes that are induced by abscisic acid and specifically expressed in the seeds will facilitate further gene discovery and a better understanding of the genetic and molecular mechanisms of seed dormancy for improving seed quality in rice breeding programs.

Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (Oryza sativa L.)

Timing of germination determines whether a new plant life cycle can be initiated; therefore, appropriate dormancy and rapid germination under diverse environmental conditions are the most important features for a seed. However, the genetic architecture of seed dormancy and germination behavior remains largely elusive. In the present study, a linkage analysis for seed dormancy and germination behavior was conducted using a set of 146 chromosome segment substitution lines (CSSLs), of which each carries a single or a few chromosomal segments of Nipponbare (NIP) in the background of Zhenshan 97 (ZS97). A total of 36 quantitative trait loci (QTLs) for six germination parameters were identified. Among them, qDOM3.1 was validated as a major QTL for seed dormancy in a segregation population derived from the qDOM3.1 near-isogenic line, and further delimited into a genomic region of 90 kb on chromosome 3. Based on genetic analysis and gene expression profiles, the candidate genes were restricted to eight genes, of which four were responsive to the addition of abscisic acid (ABA). Among them, LOC_Os03g01540 was involved in the ABA signaling pathway to regulate seed dormancy. The results will facilitate cloning the major QTLs and understanding the genetic architecture for seed dormancy and germination in rice and other crops.

Validation of QTLs for plant ideotype, earliness and growth habit traits in pigeonpea (Cajanus cajan Millsp.)

Pigeonpea productivity is greatly constrained by poor plant ideotype of existing Indian cultivars. Enhancing pigeonpea yield demands a renewed focus on restructuring the ideal plant type by using more efficient approaches like genomic tools. Therefore, the present study aims to identify and validate a set of QTLs/gene(s) presumably associated with various plant ideotype traits in pigeonpea. A total of 133 pigeonpea germplasms were evaluated along with four checks in the augmented design for various ideotype traits i.e. initiation of flowering (IF), days to 50% flowering (DFF), days to maturity (DM), plant height (PH), primary branches (PB), seeds per pod (SP) and pod length (PL). We observed significant genetic diversity in the germplasm lines for these traits. The genetic control of IF, DFF, DM and PH renders these traits suitable for detection of marker trait associations. By using residual maximum likelihood algorithm, we obtained appropriate variance-covariance structures for modeling heterogeneity, correlation of genetic effects and non-genetic residual effects. The estimates of genetic correlations indicated a strong association among earliness traits. The best linear unbiased prediction values were calculated for individual traits, and association analysis was performed in a panel of 95 diverse genotypes with 19 genic SSRs. Out of five QTL-flanking SSRs used here for validation, only ASSR295 could show significant association with FDR and Bonferroni corrections, and accounted for 15.4% IF, 14.2% DFF and 16.2% DM of phenotypic variance (PV). Remaining SSR markers (ASSR1486, ASSR206 and ASSR408) could not qualify false discovery rate (FDR) and Bonferroni criteria, hence declared as false positives. Additionally, we identified two highly significant SSR markers, ASSR8 and ASSR390 on LG 1 and LG 2, respectively. The SSR marker ASSR8 explained up to 22 and 11% PV for earliness traits and PB respectively, whereas ASSR390 controlled up to 17% PV for earliness traits. The validation and identification of new QTLs in pigeonpea across diverse genetic backgrounds brightens the prospects for marker-assisted selection to improve yield gains in pigeonpea.