Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Progress in Rice Breeding Based on Genomic Research

The role of rice genomics in breeding progress is becoming increasingly important. Deeper research into the rice genome will contribute to the identification and utilization of outstanding functional genes, enriching the diversity and genetic basis of breeding materials and meeting the diverse demands for various improvements. Here, we review the significant contributions of rice genomics research to breeding progress over the last 25 years, discussing the profound impact of genomics on rice genome sequencing, functional gene exploration, and novel breeding methods, and we provide valuable insights for future research and breeding practices.

Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages

BACKGROUND

Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. Musa acuminata, M. balbisiana and M. schizocarpa have provided the named A, B and S subgenomes that predominantly constitute these varieties. Here we aimed to characterize intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in copy-number variants (CNVs) leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterize varietal lineages better and identify sources of genetic variation.

METHODS

We delimited population structure and clonal lineages in a diverse panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination.

RESULTS

In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties.

CONCLUSIONS

We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on single nucleotide polymorphism (SNP) databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridization and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variations probably associated with phenotypic variation for future genetic studies.

Genetic Diversity and Breeding Signatures for Regional Indica Rice Improvement in Guangdong of Southern China

As the pioneer of the Green Revolution in China, Guangdong province witnessed the improvement and spread of semi-dwarf Xian/Indica rice cultivars and possessed diverse rice germplasm of landrace and cultivars. A total of 517 accessions containing a core germplasm of 479 newly sequenced landraces and modern cultivars were used to reveal breeding signatures and key variations for regional genetic improvement of indica rice from Guangdong. Four subpopulations were identified in the collection, which including Ind IV as a novel subpopulation that not covered by previously released accessions. Modern cultivars of subpopulation Ind II were inferred to have less deleterious variations, especially in yield related genes. About 15 Mb genomic segments were identified as potential breeding signatures by cross-population likelihood method (XP-CLR) of modern cultivars and landraces. The selected regions spanning multiple yield related QTLs (quantitative trait locus) which identified by GWAS (genome-wide association studies) of the same population, and specific variations that fixed in modern cultivars of Ind II were characterized. This study highlights genetic differences between traditional landraces and modern cultivars, which revealed the potential molecular basis of regional genetic improvement for Guangdong indica rice from southern China.

Population structure of Pyricularia oryzae on rice in Vietnam reveals diversified populations with four pandemic and two endemic clusters

We characterized the genetic structure of 609 strains of Pyricularia oryzae, the fungal pathogen causing rice blast disease, in three main regions in Vietnam using microsatellites (SSR) markers. From the 447 distinct multilocus genotypes identified, six genetic clusters were defined, all of them showing elevated genetic and genotypic diversities. Four of these clusters were related to rice-attacking lineages already described at the worldwide scale, whereas the two remaining clusters were endemic to Vietnam. Strains were unevenly distributed into the six clusters depending on their groups of rice variety (indica / japonica) or type of varieties (traditional / modern) of origin, but none of the clusters was specifically related to these two factors. The highest diversity of blast population was found in Northern mountainous area, and the lowest in Red River Delta in both term of genetic diversity and gene diversity. Hierarchical AMOVAs confirmed that all three factors considered (rice variety group, type of variety origin and geography) significantly contributed to the population structure of P. oryzae in Vietnam, with highest contribution from rice variety group. Mating types were unevenly distributed among clusters. Combined with results of female fertility and linkage disequilibirum, we hypothesized that clonal reproduction probably occurred in all clusters, but that sexual reproduction likely took place at least in some restricted areas in the Northern mountainous area for strains belonging to the cluster related to the previously described recombinant lineage (worldwide lineage 1). Our study pictures the genetic diversity, population structure and reproductive mode of the blast fungus in central and north Vietnam, and shows that the observed population structure is explained by several factors, the most important one being the variability of rice variety. All these new information might help for elaborating appropriate strategies to controlling the blast disease.

Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province

As a major epigenetic modification, DNA methylation plays an important role in coordinating plant responses to environmental changes. Methylation-sensitive amplified polymorphism (MSAP) technology was used in this study to investigate the epigenetic diversity of fifty japonica rice samples from five regions in Heilongjiang Province, China. In addition, the phenotypic indicators of japonica rice samples and the environmental conditions of the sampling sites were investigated and analysed. Based on the MSAP analysis technique, using eight pairs of selective primers, we identified a total of 551 amplified loci, of which 267 (48.5%) were classified as methylation loci. The methylation status and levels of the japonica rice genome in different regions differed significantly (p < 0.05). The results of the analysis of molecular variance (AMOVA) revealed that most of the molecular variation (91%) came from within the groups (regions) and was caused by individual variation within the region. Furthermore, the results of principal coordinates analysis (PCoA), cluster analysis, and population structure analysis indicated that there was no obvious correlation between the epigenetic differences and geographical locations, which may have been due to the limited range of sampling sites. When environmental factors, phenotypic indicators, and epigenetic data analysis are combined, it is easy to conclude that japonica rice grown in the same latitudinal region has increased epigenetic and phenotypic similarities due to similar climatic conditions and production practices.

Fine-scale genetic structure of the rice landrace population in Japan

Rice cultivation was introduced into Japan 3000 years ago and has expanded across the country and encompasses a wide variety of environmental conditions. Here, we elucidated the differentiation of the genetic population structure of 1037 rice landraces across Japan. Using 4451 polymorphisms derived from genome-wide analysis of double-digest restriction-site-associated DNA analysis, population genomics including ADMIXTURE and principal component analysis was carried out. These landraces were classified into nine subpopulations based on geographical origin. Massive-scale genotyping and diversity analysis demonstrated that the differentiation of genetic population structure in rice landraces across Japan might consist of two phases, namely western to eastern and southern to northern phases. The differentiation of genetic population structure was detected only in landraces from three geographical regions, Hokuriku, Tohoku, and Hokkaido, as the southern to northern phase. Conversely, differentiation was not observed in landraces from six geographical regions, Kyushu, Shikoku, Chugoku, Kinki, Tokai, and Kanto, as the western to eastern phase. The genetic population structure may have facilitated the expansion of genetic diversity among local regions.

Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam

Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index F_ST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.