Rice Genetic Diversity Research Articles

Molecular diversity of rice germplasms from Thailand characterized by different pericarp colors using Inter Simple Sequence Repeat (ISSR) markers

Abstract. Saengprajak J, Phetsom J, Sangdee A, Atichart P, Theerakulpisut P. 2024. Molecular diversity of rice germplasms from Thailand characterized by different pericarp colors using Inter Simple Sequence Repeat (ISSR) markers. Biodiversitas 25: 2839-2848. Studying genetic diversity in rice using molecular markers is necessary for varietal identification, better understanding of relationships and evolution, and conserving genetic resources. This study aimed to evaluate the genetic diversity of rice germplasms from Thailand characterized by different pericarp colors using ISSR markers. Thirty-two white and colored rice genotypes were assessed using 16 selected ISSR markers, which generated 179 alleles ranging from 210 to 1,374 bp, averaging 11.19 alleles per locus. The polymorphism percentage ranged from 40% to 100%, averaging 80%. The genetic similarity coefficient ranged from 0.458 to 0.855, while PIC values varied between 0.15 and 0.45, averaging 0.31. ISSR markers show a high Resolving Power (RP) of 12.15 and a Marker Index (MI) of 3.20, indicating their significant discriminatory power and effectiveness in detecting genetic diversity. The dendrogram grouped genotypes into five clusters: Cluster I included 5 red pericarp genotypes, Cluster II had 6 purple-black pericarp genotypes, Cluster III had 2 mixed white and purple-black pericarp genotypes, Cluster IV included 18 white pericarp genotypes, and Cluster V comprised 1 white pericarp genotype. PCA results corresponded to seed coat traits, forming eight grouping patterns similar to dendrogram clusters. These findings show that ISSR markers effectively assess genetic diversity and relationships in rice germplasms, providing valuable information for managing germplasm resources, developing variety-specific markers, and supporting rice breeding programs.

Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh.

Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed genome wide association studies (GWASs) on seven rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width, and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWASs reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain-shape-related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh-the fourth largest rice-producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.

Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study

Allelopathy has been considered as a natural method of weed control. Despite the nature of allelochemical compounds has been studied, little is known about the genetic basis underlying allelopathy. However, it is known that rice exhibits diverse allelopathic potentials across varieties, and breeding for rice plants exhibiting allelopathic potential conferring an advantage against weeds in paddy fields would be highly desirable. Knowledge of the gene factors and the identification of the genomic regions responsible for allelopathy would facilitate breeding programs. Taking advantage of the existing genetic diversity in rice, particularly in temperate japonica rice, we conducted a comprehensive investigation into the genetic determinants that contribute to rice allelopathy. Employing Genome-Wide Association Study, we identified four Quantitative Trait Loci, with the most promising loci situated on chromosome 2 and 5. Subsequent inspection of the genes located within these QTLs revealed genes associated with the biosynthesis of secondary metabolites such as Phenylalanine Ammonia Lyase (PAL), a key enzyme in the synthesis of phenolic compounds, and two genes coding for R2R3-type MYB transcription factors. The identification of these two QTLs associated to allelopathy in rice provides a useful tool for further exploration and targeted breeding strategies.

Impact of individual, combined and sequential stress on photosynthesis machinery in rice (Oryza sativa L).

Abiotic stresses such as heat, drought and submergence are major threats to global food security. Despite simultaneous or sequential occurrence of these stresses being recurrent under field conditions, crop response to such stress combinations is poorly understood. Rice is a staple food crop for the majority of human beings. Exploitation of existing genetic diversity in rice for combined and/or sequential stress is a useful approach for developing climate-resilient cultivars. We phenotyped ~400 rice accessions under high temperature, drought, or submergence and their combinations. A cumulative performance index revealed Lomello as the best performer across stress and stress combinations at the seedling stage. Lomello showed a remarkable ability to maintain a higher quantum yield of photosystem (PS) II photochemistry. Moreover, the structural integrity of the photosystems, electron flow through both PSI and PSII and the ability to protect photosystems against photoinhibition were identified as the key traits of Lomello across the stress environments. A higher membrane stability and an increased amount of leaf chlorophyll under stress may be due to an efficient management of reactive oxygen species (ROS) at the cellular level. Further, an efficient electron flow through the photosystems and, thus, a higher photosynthetic rate in Lomello is expected to act as a sink for ROS by reducing the rate of electron transport to the high amount of molecular oxygen present in the chloroplast. However, further studies are needed to identify the molecular mechanism(s) involved in the stability of photosynthetic machinery and stress management in Lomello during stress conditions.

Population Structure and Genetic Diversity of Rice (Oryza sativa L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)

Understanding the genetic diversity and population structure of rice is crucial for breeding programs, conservation efforts, and the development of sustainable agricultural practices. This study aimed to assess the genetic diversity and population structure of 94 rice (Oryza sativa L.) genotypes from the Democratic Republic of Congo using a set of 8389 high-quality DArTseq-based single nucleotide polymorphism (SNP) markers. The average polymorphic information content (PIC) of the markers was 0.25. About 42.4% of the SNPs had a PIC value between 0.25 and 0.5, which were moderately informative. The ADMIXTURE program was used for structure analysis, which revealed five sub-populations (K = 5), with admixtures. In principal component analysis (PCA), the first three principal components accounted for 36.3% of the total variation. Analysis of molecular variance revealed significant variation between sub-populations (36.09%) and within genotypes (34.04%). The low overall number of migrants (Nm = 0.23) and high fixation index (Fst = 0.52) indicated limited gene flow and significant differentiation between the sub-populations. Observed heterozygosity (Ho = 0.08) was lower than expected heterozygosity (He = 0.14) because of the high inbreeding (Fis = 0.52) nature of rice. A high average Euclidean genetic distance (0.87) revealed the existence of genetic diversity among the 94 genotypes. The significant genetic diversity among the evaluated rice genotypes can be further explored to obtain potentially desirable genes for rice improvement.

Weedy rice: An insight into genetic diversity and population structure for effective weed management

Weedy rice (Oryza sativa f. spontanea) is a conspecific weed that has invaded cultivated rice fields, effectively adapted to modern management practices, leading to substantial yield losses and reduced harvest quality. The understanding of weedy rice genetic diversity and population structure is critical in developing effective control measures. Twenty weedy rice populations were collected around the island and evaluated using 33 SSR markers. Our findings indicated that the genetic diversity (He) in a population of weedy rice was reasonably high (0.305 - 0.560). A high level of within-population (79%) and a low level of among-population (21%) genetic variation were found by analysis of molecular variance (AMOVA). There is no significant correlation across genetic and geographical distances (P>0.05). The unweighted pair group method with arithmetic mean (UPGMA) demonstrated that 20 populations were structured into two well-separated groups. Remarkably, many admixed individuals were evident according to the STRUCTURE. Weedy rice management strategies should focus on micromorphological monitoring to detect, group, and eliminate weedy rice in paddy fields, restricting the exchange of saved paddy seeds among geographical regions, increasing the production and distribution of certified seeds, the varietal recommendation for rice-growing regions to minimize mixing of varieties with different age classes, raising awareness are the recommendations to reduce the emergence of future weeds.

Study of genetic diversity in rice (Oryza sativa L.) genotypes under direct seeded condition by using principal component analysis

The present investigation was carried out to assess the genetic diversity by using principal component analysis for yield and yield contributing traits in thirty-two genotypes of rice under direct seeded condition (DSR). The experiment was conducted at Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar in randomized block design with three replications. The results revealed that first four component axes had eigen values 1.0, representing a cumulative variability of 76.86 %. Principal component analysis (PCA) indicate that four components (PC1 to PC4) accounted for about 76.86% of the total variation present among all the traits. Out of total principal components PC1, PC2, PC3 and PC4 with values 33.781%, 19.02%, 13.859% and 10.206% respectively, contributed more to the total variation. The first principal component had high positive loading for 15 traits out of 17. Similarly, second and third principal component had 7 traits each, fourth component with 6 traits had high positive loadings which contributed more to the diversity. Genotypes in cluster V showed higher mean performance for most of the yield attributing traits. Therefore, selection of parents for different traits would be effective from this cluster. Thus, result of the present study could be exploited in planning and execution of future breeding programme in rice under direct seeded condition.

Evaluation of agro-morphological traits, seed characterization and genetic diversity of local rice (Oryza sativa L.) varieties of Pakistan

Broad base genetic diversity is essential for a sustainable crop yield to provide tolerance against biotic and abiotic stresses. In Pakistan, rice is ranked second as a staple food and cultivated under different climatic zones. However, very little is known in terms of rice genetic diversity. The present research was performed to evaluate the genetic diversity among 12 local rice varieties by using 5 Simple sequence repeats (SSR) markers. Furthermore, agro-morphological parameters and seed quality of these varieties were studied. The maximum plant height (204.3 cm) and panicle length (40.1 cm) were observed for Hans-raj. The highest numbers of primary and secondary panicle branches were observed in Ratua-81 (51) and super basmati (62), respectively. Super basmati showed highest number of filled grains (264.3) and total number of grains (315) per panicle. The minimum days to maturity (140) was recorded for ratua-81 and highest 1000 grains weight (27 g) was recorded for Ksk-133. The highest concentration of elements, e.g. zinc (Zn) was observed in Ks-282 (44 µg/g), Iron (Fe) in hansraj (190.3 µg/g), manganese in bamla sufaid (111.3 µg/g), copper (Cu) in hansraj (856.3 µg/g), lead (Pb) in super basmati (3883.3 µg/g), and nickel (Ni) was found in basmati-385 (314.6 ug/g). For the genetic diversity analysis, five SSR markers were used and a total of 60 alleles were amplified with 20% polymorphism where RM28130 showed the highest Polymorphic information content (PIC) value (0.60). The maximum number of alleles (3) were produced by RM28089. Based on secondary panicle branches and total number of filled grains, Super basmati showed best panicle architecture and grain yield, which can be used in breeding program to develop high yielding aromatic rice genotypes. The highest number of filled grains and total number of grains per panicle were observed in super basmati, which indicated the potential adaptation. Basmati-2000, Hansraj, Ks-282, Super basmati and Basmati surkh-161 were found to be highly rich in micronutrients (iron, zinc, copper, lead and manganese). The maximum genetic distance was observed in basmati-2000 and basmati surkh 161 genotypes.

A Study of Genetic Variability 30 Rice Genotypes (Oryza sativa L.) Using Some SSR (Simple Sequence Repeat) Markers Adrift Zn

Rice is one of the important commodities in indonesia. Analysis of rice genetic diversity is necesarry for the succes of the local rice variety program. This study aims to identify the genetic variability and kinship patterns of 30 rice genotypes (Oryza sativa L.) using six zinc-linked SSR (Simple Sequence Repeat) markers. The research was conducted in September - December 2021 at the DNA Laboratory of the Sukamandi Rice Plant Research Center. A total of 30 local rice genotypes with diverse Zinc content have been analyzed using laboratory experiments. The results showed that there were different allele variations (2 – 8) among the genotypes tested with an average number of alleles of 4.5, while the average value of Polymorphism Information Content (PIC) amounted to 0.48 (0.20 - 0.70). 4 SSR markers have PIC values of > 0.5 (RM162, RM38, RM30, and RM80) which show that the markers are informative for the study of rice genetic diversity with Zinc content variety with an average gene diversity value of 0.53. The results of the phylogenetic analysis showed that the 30 genotypes clustered into five clusters with a similar coefficient of 0.68.

Assessment of Genetic Diversity in Rice (Oryza sativa L.) Genotypes for Grain Yield Characters

A set of 55 genotypes of rice were evaluated for “assessment of genetic diversity in rice genotypes for grain yield characters”. The experiment was conducted in a Randomized Block Design with three replications during the kharif season, of 2021 at Naini Agriculture Institute, Naini. The plant to plant distance was 15 cm and row to row distance was 20 cm. The data were recorded from five randomly selected plants for each genotypes from all the replicates for thirteen characters. Analysis of variance showed significant differences among genotypes for all 13 characters indicating that the material has adequate genetic variability to support the breeding programme for improving the grain yield of rice. Out of 55 rice genotypes evaluated for various characters, 5 genotypes were found superior for different characters. These 5 genotypes were found better for more than one character. Among the lines SHUATS DHAN -6 (62.133g) recorded the highest grain yield per hill followed by the genotypes BPT-3291 (51.8g), SHIATS Dhan -2 (51.467g), SIGNET-5455 (50.467g) and SIGNET-5455 (50.4). All these genotypes were significantly higher as compared to the check NDR - 359 (CHECK) (22.67g). High estimate of heritability coupled with high genetic advance as percent of mean was recorded for Grain yield per hill, Biological yield, Number of spikelets per panicle, Harvest Index, Flag leaf length, Number of tillers per hill, Number of panicles per hill, Flag leaf width, Test weight, and Plant height. These traits are governed by additive gene effects and therefore, may be improved through direct selection. Further the characters viz., Biological yield, Harvest Index, Number of tillers per hill, Days to fifty percent flowering, Flag leaf length and Test weight, had the highest direct positive effect and indirect effect (through each other) on grain yield per hill. Thus, selections for these characters will prove efficient for the improvement of grain yield of rice. All the 55 rice genotypes were classified using Mahalanobis D2 statistics involving 13 quantitative characters of 55 genotypes grouped into 6 clusters In the present study, the highest inter cluster distance was observed between cluster IV and cluster V (368.37) followed by cluster II and cluster V (361.04).

Molecular tools, potential frontiers for enhancing salinity tolerance in rice: A critical review and future prospective.

Improvement of salinity tolerance in rice can minimize the stress-induced yield losses. Rice (Oryza sativa) is one of Asia’s most widely consumed crops, native to the subtropical regions, and is generally associated with sensitivity to salinity stress episodes. Salt-tolerant rice genotypes have been developed using conventional breeding methods; however, the success ratio is limited because of the complex nature of the trait and the high cost of development. The narrow genetic base of rice limited the success of conventional breeding methods. Hence, it is critical to launch the molecular tools for screening rice novel germplasm for salt-tolerant genes. In this regard, the latest molecular techniques like quantitative trait loci (QTL) mapping, genetic engineering (GE), transcription factors (TFs) analysis, and clustered regularly interspaced short palindromic repeats (CRISPR) are reliable for incorporating the salt tolerance in rice at the molecular level. Large-scale use of these potent genetic approaches leads to identifying and editing several genes/alleles, and QTL/genes are accountable for holding the genetic mechanism of salinity tolerance in rice. Continuous breeding practices resulted in a huge decline in rice genetic diversity, which is a great worry for global food security. However, molecular breeding tools are the only way to conserve genetic diversity by exploring wild germplasm for desired genes in salt tolerance breeding programs. In this review, we have compiled the logical evidences of successful applications of potent molecular tools for boosting salinity tolerance in rice, their limitations, and future prospects. This well-organized information would assist future researchers in understanding the genetic improvement of salinity tolerance in rice.

Genomic Analysis Provides Insights Into the Plant Architecture Variations in in situ Conserved Chinese Wild Rice (Oryza rufipogon Griff.).

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

Global demand for rice genetic resources

BackgroundThe International Rice Research Institute (IRRI) holds in trust the world's largest collection of rice diversity, with more than 130,000 accessions of cultivated rice and wild species. Between 2012 and 2018, a total of 2174 requests for rice germplasm were received from more than 1000 unique requestors. We documented and analyzed how genebank users made use of germplasm from IRRI. As we address food and nutrition security challenges in a changing context, we are motivated by the need to enhance the conservation, management, and use of rice genetic resources.MethodsWe examined the patterns of use of the IRRI genebank using distribution data and analyzed the results from a survey of germplasm recipients. The 2019 IRRI genebank user survey is the most recent attempt to obtain structured feedback from genebank end-users in multiple countries on their use of rice germplasm since 1995. We received 244 responses (a 35% response rate) out of the complete list of 694 respondents with valid email addresses. We also tested the relationship between the availability of germplasm information, proxied by the passport data completeness index (PDCI), and the demand for rice accessions, measured by the number of requests for each unique accession using a Negative Binomial regression model. We hypothesized that materials that are better documented are more frequently requested by users because they offer more useful information for targeted research and breeding.ResultsBetween 2012 and 2018, requests for germplasm from outside IRRI were received from 63 countries in all regions of the world, mostly from Asia. IRRI distributed germplasm externally to requestors from universities (32%), national research programs (14%), private companies (9%), and individuals, including farmers (24%) as well as other CGIAR centers (3%). The traits sought most often were tolerances to environmental stresses, followed by tolerance or resistance to biotic stresses. The majority of survey respondents confirmed the usefulness of IRRI germplasm for research, breeding, characterization, and evaluation. The analytical model confirmed the significant positive relationship between PDCI values and the demand for those accessions. The results indicated that improving the availability of information at the accession level will enhance the use of those materials. To the best of our knowledge, this study is the first to show the empirical link between documentation and use of germplasm.ConclusionsThe findings demonstrate the crucial role of IRRI's genebank as a key germplasm source for global rice research and development, with important implications for the conservation and use of rice genetic diversity in the future. Public sector organizations and the scientific community in general benefit from the conservation and availability of rice genetic resources. We also show the importance of the availability of data on conserved accession to enhance their use. To sustain the benefits, continuous investment in genebanks is needed to allow them to adapt to changes in technology and agricultural context.

Characterization of Some Cultivated Rice (Oryza sativa L.) Based on Phenotypic, Physicochemical and Cooking Properties

Evaluation of rice genetic diversity is an important step for character specific varietal development program. The present study characterizes 15 rice germplasm of Indian accessions on the basis of agro morphological, physicochemical and cooking parameters. The cultivars showed high degree of variations on their traits. Mean plant height of 88.96 cm, flag leaf length (26.48 cm), flag leaf width (1.17 cm), grain per panicle ( 130), panicle length (20.97 cm), days to 50% flowering (112.06 days), kernel length breadth ratio (2.65), cooked kernel length breadth ratio (3.25), linear elongation ratio (1.65). Out of 15 rice cultivars, only Sada nunia and Das nunia are aromatic rice and Sada nunia also contain awn. Plant height showed significant positive correlation with PnL and DF and significant negative correlation with GB. GL positively significantly correlates with FLL, GrWt with GL and GB, DF with MT. The cluster analysis grouped the 15 cultivars into 4 clusters with 37.5 dissimilarity coefficient. The high variability with promising traits among the cultivars expected to be significance for future rice breeding programmes.

Morphological characterization of 3 potential lines Cempo Ireng black rice result of Gamma-Ray irradiation

Gamma-ray irradiation on Cempo Ireng can lead to the variation of morphological characteristics; hence, morphological characterization is necessary to determine changes in potential lines. This research aimed to characterize the potential lines as one of the requirements for proposing plant variety release and add black rice genetic diversity information. The research was carried out in the rice fields of Pakahan Village, Jogonalan, Klaten in January-June 2020 with the arrangement of potential lines 8,13 and 44 of M6 in a row. In total 30 plants were selected randomly for each potential line and observed 19 morphological characters. Data analysis was carried out descriptively and qualitatively with the Chi-Square test. The results showed that gamma-ray irradiation affects the characters of leaf angle, auricle color, ligule color, leaf-blade color, leaf surface, panicle type, grain color, apiculus color, and rice length. Potential line 8 had different characteristics compared to non-irradiated Cempo Ireng in the characters of auricle color, leaf-blade color, leaf width, panicle length, grain width, rice length, and rice width, while on potential lines 13 and 44 occur in the characters of the leaf surface and panicle length.

Phenotype and genotype variability of interspecific rice lines related to bacterial leaf blight resistance (Xanthomonas oryzae pv. oryzae) character

Abstract. Yuriyah S, Darnaedi D, Setia TM, Windarsih G, Utami DW. 2021. Phenotype and genotype variability of interspecific rice lines related to bacterial leaf blight resistance (Xanthomonas oryzae pv. oryzae) character. Biodiversitas 22: 4123-4130. Wild rice species are the source of the gene pool for rice genetic diversity. The cross-species crosses (interspecific crosses) play an important role in breeding, namely in terms of expanding the diversity of desirable characters, such as disease resistance and improvement in yield potential. Currently, the genes from wild rice species have been successfully introgressed into cultivated rice so that they can overcome the rice production constraints, including the introgression of genes for the bacterial leaf blight (BLB) resistance. The purpose of this study was to analyze the variability of phenotype and genotype performance of lines derived from wild rice species for the character of resistance to BLB disease. A total of 33 selected backcross lines derived from wild rice species of O. rufipogon and O. glaberrima as the donor parents and 2 control varieties (resistant and susceptible to BLB disease), were used in this study. The evaluation of phenotype and genotype of resistance characters to BLB disease was carried out during a vegetative phase of the plant. The resistance evaluation was carried out in a greenhouse, while the genotype performance was analyzed using 4 STS markers linked to Xa4, Xa7, and Xa13 genes. The result of the phenotype evaluation showed that there were variations among the resistance of the tested lines. Three lines derived from a Situ Bagendit/Oryza rufipogon cross were resistant to all BLB races used in the testing. Those three lines indicated to have the allele of the Xa7 resistance gene based on the genotype performance which grouped with the Code variety that had the Xa7 resistance gene.

Genetic diversity in rice (Oryza sativa L.) landraces of Sikkim-Himalaya and early insight into their use in genome-wide association analysis - Corrigendum

Genetic diversity in rice (Oryza sativa L.) landraces of Sikkim-Himalaya and early insight into their use in genome-wide association analysis - Corrigendum

Genetic diversity in rice (Oryza sativa L.) landraces of Sikkim-Himalaya and early insight into their use in genome-wide association analysis

AbstractThe Sikkim-Himalaya represents one of the unique reservoirs of rice genetic resources in India owing to the presence of a large number of landraces adapted to extreme climatic and edaphic conditions. This valuable gene pool is now under threat due to the introduction of high-yielding varieties, wanting suitable genetic intervention for enhancing their productivity, and thus economic viability. Development of lodging resistant, high-yielding varieties tolerant to soil acidity through association mapping aided marker-assisted breeding programmes can help achieve this in a fast and efficient manner. But this requires information on genetic diversity, population structure, etc., of the germplasm collection, which is strikingly lacking. We, therefore, characterized a set of 53 rice landraces from Sikkim to address the above issues. The results revealed moderate diversity, poor divergence and high gene flow in our germplasm collection attesting its utility as an association mapping panel. Further, a total of 115 putative marker-trait associations (P < 0.05, R2 ≥ 10%) were obtained using the general linear model and mixed linear models of which 25 were identical in both. Some of the associated markers were positioned in those regions where Qualitative Trait Loci have been previously identified in rice, providing credence to our results. The resources generated from this study will benefit the rice breeders from this region and elsewhere for targeting the yield and related traits, in addition to conservation efforts by the interested researchers.

Evolutionary Processes Involved in the Emergence and Expansion of an Atypical O. sativa Group in Madagascar

Understanding crops genetic diversity and the evolutionary processes that accompanied their worldwide spread is useful for designing effective breeding strategies. Madagascar Island was one of the last major Old World areas where human settlement brought the introduction of Oryza sativa. Early studies in the island had reported the presence of a rice group specific to Madagascar. Using 24 K SNP, we compared diversity patterns at the whole genome and at haplotype (30 SNP-long segments along the genome) levels, between 620 Malagasy and 1929 Asian rice accessions. The haplotype level analysis aimed at identifying local genotypic variations, relative to the whole genome level, using a group assignment method that relies on kernel density estimation in a Principal Component Analysis feature space. Migration bottleneck had resulted in 10–25% reduction of diversity among the Malagasy representatives of indica and japonica populations. Compared to their Asian counterpart, they showed slightly lower indica and japonica introgressions, suggesting the two populations had undergone less recombination when migration to the island occurred. The origins of the Malagasy indica and japonica groups were delineated to indica subpopulation from the Indian subcontinent and to tropical japonica from the Malay Archipelago, respectively. The Malagasy-specific group (Gm) had a rather high gene diversity and an original haplotype pattern: much lower share of indica haplotypes, and much higher share of Aus and japonica haplotypes than indica. Its emergence and expansion are most probably due to inter-group recombination facilitated by sympatry between indica-Aus admixes and “Bulu” type landraces of japonica in the central high plateaux of Madagascar, and to human selection for adaptation to the lowland rice cultivation. Pattern of rice genetic diversity was also tightly associated with the history of human settlement in the island. Emergence of the Gm group is associated with the latest arrivals of Austronesians, who founded the Merina kingdom in the high plateaux and developed lowland rice cultivation. As an intermediary form between Aus, indica and japonica, the three pillars of O. sativa domestication, Gm represents a very valuable genetic resource in breeding for adaptation to cold tolerance in tropical highlands. We proposed the name Rojo for this new rice group.

The landscape of gene–CDS–haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic improvement

Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice. We characterized the gene–coding sequence–haplotype (gcHap) diversity of 45 963 rice genes in 3010 rice accessions. With an average of 226 ± 390 gcHaps per gene in rice populations, rice genes could be classified into three main categories: 12 865 conserved genes, 10 254 subspecific differentiating genes, and 22 844 remaining genes. We found that 39 218 rice genes carry >255 179 major gcHaps of potential functional importance. Most (87.5%) of the detected gcHaps were specific to subspecies or populations. The inferred proto-ancestors of local landrace populations reconstructed from conserved predominant (ancient) gcHaps correlated strongly with wild rice accessions from the same geographic regions, supporting a multiorigin (domestication) model of Oryza sativa. Past breeding efforts generally increased the gcHap diversity of modern varieties and caused significant frequency shifts in predominant gcHaps of 14 266 genes due to independent selection in the two subspecies. Low frequencies of “favorable” gcHaps at most known genes related to rice yield in modern varieties suggest huge potential for rice improvement by mining and pyramiding of favorable gcHaps. The gcHap data were demonstrated to have greater power than SNPs for the detection of causal genes that affect complex traits. The rice gcHap diversity dataset generated in this study would facilitate rice basic research and improvement in the future.