Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits

Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province

The Honghe Hani Rice Terraces System (HHRTS) of Yunnan Province is an important agricultural and cultural heritage landscape. Until now, a large number of local rice landraces have been planted. Mining excellent genes contained in these landraces provides a reference for variety improvement and new variety breeding. In this study, 96 rice landraces collected from the Hani terraces were planted in Honghe Mengzi, Yunnan Province, in 2013, 2014, 2015, and 2021, and five major grain traits were measured and analyzed. The genomic variation of 96 rice landraces was scanned by 201 simple sequence repeat (SSR) markers. The genetic diversity, population structure, and genetic relationships of the natural population were analyzed. The mixed linear model (MLM) method of the TASSEL software was used to analyze the associations between markers and traits. A total of 936 alleles were amplified by 201 pairs of SSR primers. The average number of observed alleles (Na), the effective number of alleles (Ne), Shannon's information index (I), heterozygosity (H), and the polymorphism information content (PIC) per marker were 4.66, 2.71, 1.08, 0.15, and 0.55, respectively. Ninety-six landraces were divided into two groups by population structure, clustering, and principal component analysis, and indica rice was the main group. The coefficients of variation of the five traits ranged from 6.80 to 15.24%, and their broad heritabilities were more than 70%. In addition, there were positive correlations among the same grain traits between different years. Through MLM analysis, 2, 36, 7, 7, and 4 SSR markers were significantly associated with grain length (GL), grain width (GW), grain thickness (GT), grain length-width ratio (LWR), and thousand-grain weight (TGW), respectively. The explanation rates of phenotypic variation were 16.31 (RM449, Chr. 1)-23.51% (RM316, Chr. 9), 10.84 (RM523, Chr. 3; RM161/RM305, Chr. 5)-43.01% (RM5496, Chr. 1), 11.98 (RM161/RM305, Chr. 5)-24.72% (RM275, Chr. 6), 12.68 (RM126, Chr. 8)-36.96% (RM5496, Chr. 1), and 17.65 (RM4499, Chr. 2)-26.32% (RM25, Chr. 8), respectively. The associated markers were distributed on 12 chromosomes of the genome.

Evaluation of gene flow and genetic diversity in rice accessions across Kurdistan region-iraq using SSR markers

Background

In recent years, farmers have complained that the only way to obtain seeds is to select plants that show good performance under local climate conditions in the region. This study aimed to investigate the diversity of rice accessions grown in the region to build a breeding program.

Methods and results

A total of 62 accessions of rice from farmers and research stations were collected from the Kurdistan region, including short-grain and long-grain types, for molecular genetics and diversity analysis. In this study, 37 polymorphic simple sequence repeat (SSR) markers were selected with several molecular genetics software programs. The results show that these SSR markers are very effective for this investigation, generating a total of 152 observed alleles (Na), 75.166 Effective number of alleles (Ne) and an average of 4.1 and 2.03 alleles per locus, respectively. The average polymorphic information content (PIC) per locus was recorded as 0.404. The research presented here confirms two subpopulations, japonica (C1 and C2) and indica (C3), based on molecular genetics data analysis. Analysis of molecular variance revealed that the 72% variance was due to the variation among populations and 28% within the population.

Conclusions

Altogether, these results indicate that there is very low gene flow. These results show the importance of the study of genetic diversity and relationships for starting breeding and improvement programs for rice in the Kurdistan region.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11033-021-06920-x.

Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping

Background

Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population.

Results

The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg^− 1, ranging from 0.22 mg.mg-¹ to 0.93 mg.mg^− 1, with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg^− 1 (RM7309–135 bp on chromosome 9) to 0.45 mg.mg^− 1 (RM297–180 bp on chromosome 2). RM297–180 bp showed the largest phenotypic effect value (0.44 mg.mg^− 1 in 2016 and 0.45 mg.mg^− 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297–175 bp (0.43 mg.mg^− 1 in 2016 and 0.44 mg.mg^− 1 in 2017).

Conclusion

Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.

InDel Marker Based Estimation of Multi-Gene Allele Contribution and Genetic Variations for Grain Size and Weight in Rice (Oryza sativa L.)

The market success of any rice cultivar is exceedingly dependent on its grain appearance, as well as its grain yield, which define its demand by consumers as well as growers. The present study was undertaken to explore the contribution of nine major genes, qPE9~1, GW2, SLG7, GW5, GS3, GS7, GW8, GS5, and GS2, in regulating four size and weight related traits, i.e., grain length (GL), grain width (GW), grain thickness (GT), and thousand grain weight (TGW) in 204 diverse rice germplasms using Insertion/Deletion (InDel) markers. The studied germplasm displayed wide-ranging variability in the four studied traits. Except for three genes, all six genes showed considerable association with these traits with varying strengths. Whole germplasm of 204 genotypes could be categorized into three major clusters with different grain sizes and weights that could be utilized in rice breeding programs where grain appearance and weight are under consideration. The study revealed that TGW was 24.9% influenced by GL, 37.4% influenced by GW, and 49.1% influenced by GT. Hence, assuming the trend of trait selection, i.e., GT > GW > GL, for improving TGW in the rice yield enhancement programs. The InDel markers successfully identified a total of 38 alleles, out of which 27 alleles were major and were found in more than 20 genotypes. GL was associated with four genes (GS3, GS7, GW8, and GS2). GT was also found to be regulated by four different genes (GS3, GS7, GW8, and GS2) out of the nine studied genes. GW was found to be under the control of three studied genes (GW5, GW8, and GS2), whereas TGW was found to be under the influence of four genes (SLG7, GW5, GW8, and GS5) in the germplasm under study. The Unweighted Pair Group Method with Arithmetic means (UPGMA) tree based on the studied InDel marker loci segregated the whole germplasm into three distinct clusters with dissimilar grain sizes and weights. A two-dimensional scatter plot constructed using Principal Coordinate Analysis (PCoA) based on InDel markers further separated the 204 rice germplasms into four sub-populations with prominent demarcations of extra-long, long, medium, and short grain type germplasms that can be utilized in breeding programs accordingly. The present study could help rice breeders to select a suitable InDel marker and in formulation of breeding strategies for improving grain appearance, as well as weight, to develop rice varieties to compete international market demands with higher yield returns. This study also confirms the efficient application of InDel markers in studying diverse types of rice germplasm, allelic frequencies, multiple-gene allele contributions, marker-trait associations, and genetic variations that can be explored further.

Analysis of genetic diversity and population structure using SSR markers and validation of a Cleavage Amplified Polymorphic Sequences (CAPS) marker involving the sodium transporter OsHKT1;5 in saline tolerant rice (Oryza sativa L.) landraces

Naturally evolved saline tolerant rice landraces found along the coastline of India are a valuable genomic resource to explore the complex, polygenic nature of salinity tolerance. In the present study, a set of 28 genome wide SSR markers, 11 salt responsive genic SSR markers and 8 Saltol QTL linked SSR markers were used to estimate genetic relatedness and population structure within a collection of 47 rice landraces (including a tolerant and 2 sensitive checks) originating from geographically divergent coastal regions of India. All three marker types identified substantial genetic variation among the landraces, as evident from their higher PIC values (0.53 for genomic SSRs, 0.43 for Genic SSRs and 0.59 for Saltol SSRs). The markers RM431, RM484 (Genomic SSRs), OsCAX (D), OsCAX (T) (Genic SSRs) and RM562 (Saltol SSR) were identified as good candidates to be used in breeding programs for improving salinity tolerance in rice. STRUCTURE analysis divided the landraces into five distinct populations, with classification correlating with their geographical locations. Principal coordinate and hierarchical cluster analyses (UPGMA and neighbor joining) are in close agreement with STRUCTURE results. AMOVA analysis indicated a higher magnitude of genetic differentiation within individuals of groups (58%), than among groups (42%). We also report the development and validation of a new Cleavage Amplified Polymorphic Sequence (CAPS) marker (OsHKT1;5V395) that targets a codon in the sodium transporter gene OsHKT1;5 (Saltol/SKC1 locus) that is associated with sodium transport rates in the above rice landraces. The CAPS marker was found to be present in all landraces except in IR29, Kamini, Gheus, Matla 1 and Matla 2. Significant molecular genetic diversity established among the analyzed salt tolerant rice landraces will aid in future association mapping; the CAPS marker, OsHKT1;5V395 can be used to map rice landraces for the presence of the SNP (Single Nucleotide Polymorphism) associated with increased sodium transport rates and concomitant salinity tolerance in rice.

Identification of QTLs for rice grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari

Grain size is important for brewing-rice cultivars, but the genetic basis for this trait is still unclear. This paper aims to identify QTLs for grain size using novel chromosomal segment substitution lines (CSSLs) harboring chromosomal segments from Yamadanishiki, an excellent sake-brewing rice, in the genetic background of Koshihikari, a cooking cultivar. We developed a set of 49 CSSLs. Grain length (GL), grain width (GWh), grain thickness (GT), 100-grain weight (GWt) and days to heading (DTH) were evaluated, and a CSSL-QTL analysis was conducted. Eighteen QTLs for grain size and DTH were identified. Seven (qGL11, qGWh5, qGWh10, qGWt6-2, qGWt10-2, qDTH3, and qDTH6) that were detected in F₂ and recombinant inbred lines (RILs) from Koshihikari/Yamadanishiki were validated, suggesting that they are important for large grain size and heading date in Yamadanishiki. Additionally, QTL reanalysis for GWt showed that qGWt10-2 was only detected in early-flowering RILs, while qGWt5 (in the same region as qGWh5) was only detected in late-flowering RILs, suggesting that these QTLs show different responses to the environment. Our study revealed that grain size in the Yamadanishiki cultivar is determined by a complex genetic mechanism. These findings could be useful for the breeding of both cooking and brewing rice.

Genetic loci simultaneously controlling lignin monomers and biomass digestibility of rice straw

Lignin content and composition are crucial factors affecting biomass digestibility. Exploring the genetic loci simultaneously affecting lignin-relevant traits and biomass digestibility is a precondition for lignin genetic manipulation towards energy crop breeding. In this study, a high-throughput platform was employed to assay the lignin content, lignin composition and biomass enzymatic digestibility of a rice recombinant inbred line population. Correlation analysis indicated that the absolute content of lignin monomers rather than lignin content had negative effects on biomass saccharification, whereas the relative content of p-hydroxyphenyl unit and the molar ratio of p-hydroxyphenyl unit to guaiacyl unit exhibited positive roles. Eight QTL clusters were identified and four of them affecting both lignin composition and biomass digestibility. The additive effects of clustered QTL revealed consistent relationships between lignin-relevant traits and biomass digestibility. Pyramiding rice lines containing the above four positive alleles for increasing biomass digestibility were selected and showed comparable lignin content, decreased syringyl or guaiacyl unit and increased molar percentage of p-hydroxyphenyl unit, the molar ratio of p-hydroxyphenyl unit to guaiacyl unit and sugar releases. More importantly, the lodging resistance and eating/cooking quality of pyramiding lines were not sacrificed, indicating the QTL information could be applied to select desirable energy rice lines.

Favorable Marker Alleles for Panicle Exsertion Length in Rice (Oryza sativa L.) Mined by Association Mapping and the RSTEP-LRT Method

The panicle exsertion length (PEL) in rice (Oryza sativa L.) is an important trait for hybrid seed production. We investigated the PEL in a chromosome segment substitution line (CSSL) population consisting of 66 lines and a natural population composed of 540 varieties. In the CSSL population, a total of seven QTLs for PEL were detected across two environments. The percentage of phenotypic variance explained (PVE) ranged from 10.22 to 50.18%, and the additive effect ranged from -1.77 to 6.47 cm. Among the seven QTLs, qPEL10.2 had the largest PVE, 44.05 and 50.18%, with an additive effect of 5.91 and 6.47 cm in 2015 and in 2016, respectively. In the natural population, 13 SSR marker loci were detected that were associated with PEL in all four environments, with the PVE ranging from 1.20 to 6.26%. Among the 13 loci, 7 were novel. The RM5746-170 bp allele had the largest phenotypic effect (5.11 cm), and the typical carrier variety was Qiaobinghuang. An RM5620-RM6100 region harboring the EUI2 locus on chromosome 10 was detected in both populations. The sequencing results showed that the accessions with a shorter PEL contained the A base, while the accessions with a longer PEL contained the G base at the 1,475 bp location of the EUI2 gene.

Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping

BACKGROUND

Poor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice.

RESULTS

In this study, the GP of 177 rice varieties was investigated in three locations across 2 years. By combining the genotype data of 261 simple sequence repeat (SSR) markers, association mapping was conducted to identify the marker-GP association loci. Among 31 marker-GP association loci detected in two or more environments and determined using general linear model (GLM) analyses, seven association loci were also detected using mixed linear model (MLM) analyses. The seven common loci detected by the two analytical methods were located on chromosomes 2, 3 (2), 7, 8 and 12 (2) and explained 7.24~22.28% of the variance. Of these 7 association loci, five markers linked to GP were newly detected: RM5340 on Chr2, RM5480 and RM148 on Chr3, RM1235 on Chr8, and RM5479 on Chr12.

CONCLUSIONS

Five marker-GP association loci were newly detected using both the GLM and MLM analytical methods. Elite allele RM505-170 bp had the highest average phenotypic effect on increasing the GP, and the typical carrier variety was 'Maozitou'. Based on the distribution of the elite alleles among the carrier varieties, the top 10 parental combinations for improving the GP in rice via cross-breeding were predicted.

Identification and Characterization of Quantitative Trait Loci for Shattering in Rice Landrace Jiucaiqing from Taihu Lake Valley, China

Easy shattering reduces yield from grain loss during rice ( L.) harvest. We characterized a nonshattering rice landrace Jiucaiqing from Taihu Lake valley in China. The breaking tensile strength (BTS; grams force, gf) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering at 0, 7, 14, 21, 28, and 35 d after heading (DAH). The BTS of Jiucaiqing did not significantly decrease with increasing DAH, maintaining a level of 152.2 to 195.9 gf, while that of IR26 decreased greatly during 0 to 14 DAH and finally stabilized at ∼100 gf. Then the chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) of Jiucaiqing in IR26 background were developed for quantitative trait loci (QTL) mapping. Four putative QTL (, , , and ) for shattering were detected, and the was confirmed on chromosome 1. We further mapped to a 98.4-kb region, which contains 14 genes. Os01g62920 was considered to be a strong candidate for , which colocated with . Further quantitative real-time polymerase chain reaction (PCR) analyses confirmed that the QTL can significantly decrease the expression of shattering related genes (, , , , and ) especially at the middle development stage at 10 and 15 cm panicle length, which causes rice shattering decrease. The elite allele and the NIL with desirable agronomic traits identified in this study could be useful for rice breeding.

QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping

Stigma traits are very important for hybrid seed production in Oryza sativa, which is a self-pollinated crop; however, the genetic mechanism controlling the traits is poorly understood. In this study, we investigated the phenotypic data of 227 accessions across 2 years and assessed their genotypic variation with 249 simple sequence repeat (SSR) markers. By combining phenotypic and genotypic data, a genome-wide association (GWA) map was generated. Large phenotypic variations in stigma length (STL), stigma brush-shaped part length (SBPL) and stigma non-brush-shaped part length (SNBPL) were found. Significant positive correlations were identified among stigma traits. In total, 2072 alleles were detected among 227 accessions, with an average of 8.3 alleles per SSR locus. GWA mapping detected 6 quantitative trait loci (QTLs) for the STL, 2 QTLs for the SBPL and 7 QTLs for the SNBPL. Eleven, 5, and 12 elite alleles were found for the STL, SBPL, and SNBPL, respectively. Optimal cross designs were predicted for improving the target traits. The detected genetic variation in stigma traits and QTLs provides helpful information for cloning candidate STL genes and breeding rice cultivars with longer STLs in the future.

Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping

Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes.