Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding

The era of panomics-driven gene discovery in plants

Panomics is an approach to integrate multiple 'omics' datasets, generated using different individuals or natural variations. Considering their diverse phenotypic spectrum, the phenome is inherently associated with panomics-based science, which is further combined with genomics, transcriptomics, metabolomics, and other omics techniques, either independently or collectively. Panomics has been accelerated through recent technological advancements in the field of genomics that enable the detection of population-wide structural variations (SVs) and hence offer unprecedented insights into the genetic variations contributing to important agronomic traits. The present review provides the recent trends of panomics-driven gene discovery toward various traits related to plant development, stress tolerance, accumulation of specialized metabolites, and domestication/dedomestication. In addition, the success stories are highlighted in the broader context of enhancing crop productivity.

Dissecting the molecular basis of the ultra-large grain formation in rice

The shape of rice grains not only determines the thousand-grain weight but also correlates closely with the grain quality. Here we identified an ultra-large grain accession (ULG) with a thousand-grain weight exceeding 60 g. The integrated analysis of QTL, BSA, de novo genome assembled, transcription sequencing, and gene editing was conducted to dissect the molecular basis of the ULG formation. The ULG pyramided advantageous alleles from at least four known grain-shaping genes, OsLG3, OsMADS1, GS3, GL3.1, and one novel locus, qULG2-b, which encoded a leucine-rich repeat receptor-like kinase. The collective impacts of OsLG3, OsMADS1, GS3, and GL3.1 on grain size were confirmed in transgenic plants and near-isogenic lines. The transcriptome analysis identified 112 genes cooperatively regulated by these four genes that were prominently involved in photosynthesis and carbon metabolism. By leveraging the pleiotropy of these genes, we enhanced the grain yield, appearance, and stress tolerance of rice var. SN265. Beyond showcasing the pyramiding of multiple grain size regulation genes that can produce ULG, our study provides a theoretical framework and valuable genomic resources for improving rice variety by leveraging the pleiotropy of grain size regulated genes.

Enhancing grain shape, thermotolerance, and alkaline tolerance via Gγ protein manipulation in rice

KEY MESSAGE

Our findings highlight a valuable breeding resource, demonstrating the potential to concurrently enhance grain shape, thermotolerance, and alkaline tolerance by manipulating Gγ protein in rice. Temperate Geng/Japonica (GJ) rice yields have improved significantly, bolstering global food security. However, GJ rice breeding faces challenges, including enhancing grain quality, ensuring stable yields at warmer temperatures, and utilizing alkaline land. In this study, we employed CRISPR/Cas9 gene-editing technology to knock out the GS3 locus in seven elite GJ varieties with superior yield performance. Yield component measurements revealed that GS3 knockout mutants consistently enhanced grain length and reduced plant height in diverse genetic backgrounds. The impact of GS3 on the grain number per panicle and setting rate depended on the genetic background. GS3 knockout did not affect milling quality and minimally altered protein and amylose content but notably influenced chalkiness-related traits. GS3 knockout indiscriminately improved heat and alkali stress tolerance in the GJ varieties studied. Transcriptome analysis indicated differential gene expression between the GS3 mutants and their wild-type counterparts, enriched in biological processes related to photosynthesis, photosystem II stabilization, and pathways associated with photosynthesis and cutin, suberine, and wax biosynthesis. Our findings highlight GS3 as a breeding resource for concurrently improving grain shape, thermotolerance, and alkaline tolerance through Gγ protein manipulation in rice.

The Landscape of Presence/Absence Variations during the Improvement of Rice

Rice is one of the most important staple crops in the world; therefore, the improvement of rice holds great significance for enhancing agricultural production and addressing food security challenges. Although there have been numerous studies on the role of single-nucleotide polymorphisms (SNPs) in rice improvement with the development of next-generation sequencing technologies, research on the role of presence/absence variations (PAVs) in the improvement of rice is limited. In particular, there is a scarcity of studies exploring the traits and genes that may be affected by PAVs in rice. Here, we extracted PAVs utilizing resequencing data from 148 improved rice varieties distributed in Asia. We detected a total of 33,220 PAVs and found that the number of variations decreased gradually as the length of the PAVs increased. The number of PAVs was the highest on chromosome 1. Furthermore, we identified a 6 Mb hotspot region on chromosome 11 containing 1091 PAVs in which there were 29 genes related to defense responses. By conducting a genome-wide association study (GWAS) using PAV variation data and phenotypic data for five traits (flowering time, plant height, flag leaf length, flag leaf width, and panicle number) across all materials, we identified 186 significantly associated PAVs involving 20 cloned genes. A haplotype analysis and expression analysis of candidate genes revealed that important genes might be affected by PAVs, such as the flowering time gene OsSFL1 and the flag leaf width gene NAL1. Our work investigated the pattern in PAVs and explored important PAV key functional genes associated with agronomic traits. Consequently, these results provide potential and exploitable genetic resources for rice breeding.

A comprehensive lettuce variation map reveals the impact of structural variations in agronomic traits

BACKGROUND

As an important vegetable crop, cultivated lettuce is grown worldwide and a great variety of agronomic traits have been preserved within germplasm collections. The mechanisms underlying these phenotypic variations remain to be elucidated in association with sequence variations. Compared with single nucleotide polymorphisms, structural variations (SVs) that have more impacts on gene functions remain largely uncharacterized in the lettuce genome.

RESULTS

Here, we produced a comprehensive SV set for 333 wild and cultivated lettuce accessions. Comparison of SV frequencies showed that the SVs prevalent in L. sativa affected the genes enriched in carbohydrate derivative catabolic and secondary metabolic processes. Genome-wide association analysis of seven agronomic traits uncovered potentially causal SVs associated with seed coat color and leaf anthocyanin content.

CONCLUSION

Our work characterized a great abundance of SVs in the lettuce genome, and provides a valuable genomic resource for future lettuce breeding.

A chromosome-level genome assembly of an early matured aromatic Japonica rice variety Qigeng10 to accelerate rice breeding for high grain quality in Northeast China

Early-matured aromatic japonica rice from the Northeast is the most popular rice commodity in the Chinese market. The Qigeng10 (QG10) was one of the varieties with the largest planting area in this region in recent years. It was an early-matured japonica rice variety with a lot of superior traits such as semi-dwarf, lodging resistance, long grain, aromatic and good quality. Therefore, a high-quality assembly of Qigeng10 genome is critical and useful for japonica research and breeding. In this study, we produced a high-precision QG10 chromosome-level genome by using a combination of Nanopore and Hi-C platforms. Finally, we assembled the QG10 genome into 77 contigs with an N50 length of 11.80 Mb in 27 scaffolds with an N50 length of 30.55 Mb. The assembled genome size was 378.31Mb with 65 contigs and constituted approximately 99.59% of the 12 chromosomes. We identified a total of 1,080,819 SNPs and 682,392 InDels between QG10 and Nipponbare. We also annotated 57,599 genes by the Ab initio method, homology-based technique, and RNA-seq. Based on the assembled genome sequence, we detected the sequence variation in a total of 63 cloned genes involved in grain yield, grain size, disease tolerance, lodging resistance, fragrance, and many other important traits. Finally, we identified five elite alleles (qTGW2^Nipponbare , qTGW3^Nanyangzhan , GW5^IR24 , GW6^Suyunuo , and qGW8^Basmati385 ) controlling long grain size, four elite alleles (COLD1^Nipponbare , bZIP73^Nipponbare , CTB4a^{Kunmingxiaobaigu} , and CTB2^{Kunmingxiaobaigu} ) controlling cold tolerance, three non-functional alleles (DTH7^Kitaake , Ghd7^Hejiang19 , and Hd1^Longgeng31 ) for early heading, two resistant alleles (Pia^Akihikari and Pid4^Digu ) for rice blast, a resistant allele STV11^Kasalath for rice stripe virus, an NRT1.1B^IR24 allele for higher nitrate absorption activity, an elite allele SCM3^Chugoku117 for stronger culms, and the typical aromatic gene badh2-E2 for fragrance in QG10. These results not only help us to better elucidate the genetic mechanisms underlying excellent agronomic traits in QG10 but also have wide-ranging implications for genomics-assisted breeding in early-matured fragrant japonica rice.

Photoperiod Genes Contribute to Daylength-Sensing and Breeding in Rice

Rice (Oryza sativa L.), one of the most important food crops worldwide, is a facultative short-day (SD) plant in which flowering is modulated by seasonal and temperature cues. The photoperiodic molecular network is the core network for regulating flowering in rice, and is composed of photoreceptors, a circadian clock, a photoperiodic flowering core module, and florigen genes. The Hd1-DTH8-Ghd7-PRR37 module, a photoperiodic flowering core module, improves the latitude adaptation through mediating the multiple daylength-sensing processes in rice. However, how the other photoperiod-related genes regulate daylength-sensing and latitude adaptation remains largely unknown. Here, we determined that mutations in the photoreceptor and circadian clock genes can generate different daylength-sensing processes. Furthermore, we measured the yield-related traits in various mutants, including the main panicle length, grains per panicle, seed-setting rate, hundred-grain weight, and yield per panicle. Our results showed that the prr37, elf3-1 and ehd1 mutants can change the daylength-sensing processes and exhibit longer main panicle lengths and more grains per panicle. Hence, the PRR37, ELF3-1 and Ehd1 locus has excellent potential for latitude adaptation and production improvement in rice breeding. In summary, this study systematically explored how vital elements of the photoperiod network regulate daylength sensing and yield traits, providing critical information for their breeding applications.

Introgression of a Complex Genomic Structural Variation Causes Hybrid Male Sterility in GJ Rice (Oryza sativa L.) Subspecies

Hybrids between different subspecies of rice Oryza sativa L. commonly show hybrid sterility. Here we show that a widely planted commercial japonica/GJ variety, DHX2, exhibited hybrid sterility when crossing with other GJ varieties. Using the high-quality genome assembly, we identified three copies of the Sc gene in DHX2, whereas Nipponbare (Nip) had only one copy of Sc. Knocking out the extra copies of Sc in DHX2 significantly improved the pollen fertility of the F1 plant of DHX2/Nip cross. The population structure analysis revealed that a slight introgression from Basmati1 might occur in the genome of DHX2. We demonstrated that both DHX2 and Basmati1 harbored three copies of Sc. Moreover, the introgression of GS3 and BADH2/fgr from Basmati1 confers the slender and fragrance grain of DHX2. These results add to our understanding of the hybrid sterility of inter-subspecies and intra-subspecies and may provide a novel strategy for hybrid breeding.