Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars

Cui, Di; Zhou, Han; Ma, Xiaoding; Lin, Zhou; Sun, Landi; Han, Bing; Li, Maomao; Sun, Jingli; Liu, Jin; Jin, Guixiu; Wang, Xianju; Cao, Guilan; Deng, Xing Wang; He, Hang; Han, Longzhi

doi:10.1016/j.xplc.2022.100325

Cited by 9 publications

(6 citation statements)

References 102 publications

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“…Genetic diversity was higher in the G1 than in the G2 subpopulation; 91.15% of the germplasm in subpopulation G1 were from Jilin and Liaoning, China, whereas most of the germplasm in subpopulation G2 came from Japan and Heilongjiang, China. Previous studies have shown that japonica varieties from Jilin and Liaoning have higher levels of introgression of indica consanguinity from the breeding process than japonica varieties from Japan and Heilongjiang do ( Cui et al., 2022 ). Thus, the genetic diversity of subpopulation G1 was higher due to the introgression of a higher proportion of indica consanguinity.…”

Section: Discussionmentioning

confidence: 95%

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Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study

Han

et al. 2022

Front. Plant Sci.

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Salt stress affects rice seed germination and seedling formation, seriously restricting rice production. Screening salt-tolerant rice varieties and analyzing the genetic mechanisms underlying salt tolerance are therefore very important to ensure rice production. In this study, 313 Oryza sativa ssp. japonica germplasm were used to conduct a genome-wide association study (GWAS) using 1% NaCl as a salt stress treatment during germination stage. The germination potential (GP) on different days and the germination index (GI) under salt stress were used as salt tolerance indicators. The results of population structure analysis showed that the 313 germplasm studied could be divided into two subpopulations, consistent with the geographical origins of the materials. There were 52 loci significantly related to salt tolerance during germination, and the phenotypic contribution rate of 29 loci was > 10%. A region on chromosome 11 (17049672–17249672 bp) was repeatedly located, and the candidate gene LOC_Os11g29490, which encodes a plasma membrane ATPase, was identified in this locus. Further haplotype analysis showed the GP of germplasm with different haplotypes at that locus significantly differed under salt stress (p < 0.05), and germplasm carrying Hap2 displayed strong salt tolerance during the germination stage. Two other promising candidate genes for salt tolerance were identified: LOC_Os01g27170 (OsHAK3), which encodes a potassium transporter, and LOC_Os10g42550 (OsITPK5), which encodes an inositol 1, 3, 4-trisphosphate 5/6-kinase. The results of this study provide a theoretical basis for salt-tolerant gene cloning and molecular design breeding in rice.

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Section: Discussionmentioning

confidence: 95%

“…The raw sequence data reported in this paper have been deposited in the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), under accession codes CRA004238 ( ). The average sequencing depth and average genome coverage of these data were 25.60× and 90.29%, respectively ( Cui et al., 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study

Han

et al. 2022

Front. Plant Sci.

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“…In an investigation of 1200 Chinese accessions, an average of 6.8 Mb XI genome introgression was found in GJ accessions [ 26 ]. Notably, the important gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1 , SMG1 , DEP3 , Pib , Pi-d 2, and Bph3 , were introduced from XI rice to GJ by introgression [ 27 ]. In this study, we found that there is cB introgression in some Chinese GJ varieties, such as DHX2.…”

Section: Discussionmentioning

confidence: 99%

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

Xu¹,

Xu²,

Xu³

et al. 2022

IJMS

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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.

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“…The japonica/Geng rice planting area is 9.87 million ha, accounting for approximately 32.9 percent of the total rice planting area in China (Tang and Chen, 2021). Recently, the early-matured japonica/Geng rice is becoming more and more important, and its growing area was more than 4 million ha in Northeast China (Cui et al, 2022). Two genome draft sequences of the cultivated rice subspecies japonica/Geng Nipponbare and Indica/Xian 93-11 were released in 2002 (Goff et al, 2002;Yu et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

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

Jiang

Zhang²,

Xin³

et al. 2023

Front. Plant Sci.

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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 (qTGW2Nipponbare, qTGW3Nanyangzhan, GW5IR24, GW6Suyunuo, and qGW8Basmati385) controlling long grain size, four elite alleles (COLD1Nipponbare, bZIP73Nipponbare, CTB4aKunmingxiaobaigu, and CTB2Kunmingxiaobaigu) controlling cold tolerance, three non-functional alleles (DTH7Kitaake, Ghd7Hejiang19, and Hd1Longgeng31) for early heading, two resistant alleles (PiaAkihikari and Pid4Digu) for rice blast, a resistant allele STV11Kasalath for rice stripe virus, an NRT1.1BIR24 allele for higher nitrate absorption activity, an elite allele SCM3Chugoku117 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.

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Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars

Cited by 9 publications

References 102 publications

Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study

Candidate gene discovery for salt tolerance in rice (Oryza sativa L.) at the germination stage based on genome-wide association study

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

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

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