Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L

A pangenome reference of wild and cultivated rice

Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence-absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.

Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated rice Oryza sativa L

Anagenesis accumulates favorable mutations that enable crops to adapt to continually improving artificial production environments, while cladogenesis results in the deposition of beneficial variations across diverse ecotypes. Integrating advantageous genetic variations from diverse evolutionary sources establishes the foundation for the continued genetic improvement of crops. For a long time, rice breeding practices have been guided by the established belief that the Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and subsp. japonica. Integrating elite genetic variants from both subspecies has been a major strategy for genetic improvement. This approach has proven successful through the achievements of temperate japonica breeding programs in China, Japan, and Korea over the past decades. The genetic differentiation within the Asian cultivated rice has been successfully harnessed for heterosis breeding, thereby enhancing rice yield productivity. Genomic investigations have revealed more genetic divergences in the Asian cultivated rice, prompting the proposal of six subgroups within it. This indicates that there is greater potential for uncovering additional genetic divergences and diversity in future breeding practices. Genetic introgression and gene flow among subgroups have led to improvements in agronomic traits within the indica, temperate japonica, and tropical japonica subgroups during the modern rice breeding process. The introgression process has widened the genetic diversity within subgroups and reduced the genetic distance between them, resulting in the creation of new genetic blocks and subpopulations. Artificial introgression has accelerated the evolution process in rice breeding history. Advancements in the study of genetic divergence and diversity in rice offer valuable insights to guide breeding practices. The mini subgroups aus, basmatic, and rayada possess untapped genetic potential but have been poorly studied worldwide; more samples should be further investigated. This information will be invaluable for harnessing these advantageous variations through introgression breeding. Further studying the nature of reproductive barriers among subgroups will enhance our understanding of genetic differentiation, allow us to overcome these barriers and facilitate effective genetic exchange, and even enable us to harness heterosis among subgroups.

Revisiting development and physiology of wild rice relatives for crop improvement and climate resilience

KEY MESSAGE

The review summarizes developmental and physiologic traits of wild rice relatives that can be targeted in mainstream rice-improvement programs for yield increases under changing climate. Increasing rice yield and productivity under changing climatic conditions is imperative for sustainable food security, given rice is a major staple crop around the world. Natural variation in crop plants, including wild relatives, offers remarkable genetic variability to explore the desirable developmental and physiologic traits for crop improvement. Wild relatives of rice, with distinct developmental and physiologic features compared to cultivated varieties, are the potential genetic and genomic resource for rice yield increases under changing climate. A thorough genetic basis of rice developmental and architectural changes during domestication is now established with the identification and characterization of domestication genes. Photosynthetically efficient wild rice accessions, with desirable developmental, physiologic, and metabolic traits, have been identified in recent years that could be instrumental for rice improvement. While several abiotic and biotic stress-tolerant wild relatives of rice along with the associated genetic loci have been identified over the years, a comprehensive insight into the desirable developmental and physiologic attributes of the wild rice is limited. Moreover, the usage of wild rice is not streamlined in rice-improvement programs due to genetic and genomic constraints. In this review, we summarize the desirable developmental and physiologic features of wild rice species that can be exploited for combining yield increases with climate resilience in rice-improvement programs.

Identification of a novel hybrid sterility locus S67 between temperate japonica subgroup and basmati subgroup in Oryza sativa L

Asian cultivated rice (Oryza sativa L.) is the most important cultivated species in the AA genome species of the genus Oryza. basmati is a special and famous subgroup in Asian cultivated rice, and temperate japonica is one of the most important cultivated subgroup, too. However, hybrid sterility hinders the introgression of favorable traits and the utilization of hybrid vigour between the two subgroups. The genetic basis of intraspecific hybrid sterility between temperate japonica and basmati remained elusive. In this study, a novel hybrid sterility locus S67 was identified, which caused hybrid male sterility in hybrids between the temperate japonica rice variety Dianjingyou 1 (DJY1) and the basmati rice variety Dom-sufid. Initial mapping with BC1F1, BC4F1, BC4F2 populations and DNA markers located S67 between RM5362 and K1-40.6 on the long arm of chromosome 1. Genetic analysis confirmed that S67 caused a transmission advantage for the temperate japonica rice S67-te allele in the hybrid offsprings. This result not only fills the gap in the research on hybrid sterility between basmati and temperate japonica, but also lays a good foundation for the systematic study of the genetic nature of hybrid sterility between basmati and other subgroups, as well as the full exploration and utilization of this subgroup through the creation of wide or specific compatibility lines to overcome hybrid sterility. In addition, this result can also help us broaden our understanding of genetic differentiation within Asian cultivated rice and hybrid sterility between inter-subgroups.

Hybridization and introgression events in cooccurring populations of closely related grasses (Poaceae: Stipa) in high mountain steppes of Central Asia

Stipa is a genus comprising ca. 150 species found in warm temperate regions of the Old World and around 30% of its representatives are of hybrid origin. In this study, using integrative taxonomy approach, we tested the hypothesis that hybridization and introgression are the explanations of the morphological intermediacy in species belonging to Stipa sect. Smirnovia, one of the species-rich sections in the mountains of Central Asia. Two novel nothospecies, S. magnifica × S. caucasica subsp. nikolai and S. lingua × S. caucasica subsp. nikolai, were identified based on a combination of morphological characters and SNPs markers. SNPs marker revealed that all S. lingua × S. caucasica samples were F1 hybrids, whereas most of S. magnifica × S. caucasica samples were backcross hybrids. Furthermore, the above mentioned hybrids exhibit transgressive morphological characters to each of their parental species. These findings have implications for understanding the process of hybridization in the genus Stipa, particularly in the sect. Smirnovia. As a taxonomic conclusion, we describe the two new nothospecies S. × muksuensis (from Tajikistan) and S. × ochyrae (from Kyrgyzstan) and present an identification key to species morphologically similar to the taxa mentioned above.

A derived weedy rice × ancestral cultivar cross identifies evolutionarily relevant weediness QTLs

Weedy rice (Oryza spp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved from aus cultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL-seq approach that combines bulked segregant analysis and high-throughput whole genome resequencing to map the three important weediness traits in an F2 population derived from a cross between BHA weedy rice with an ancestral aus cultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop, indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor-descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa.