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Li F, Wu L, Li X, Chai Y, Ruan N, Wang Y, Xu N, Yu Z, Wang X, Chen H, Lu J, Xu H, Xu Z, Chen W, Xu Q. Dissecting the molecular basis of the ultra-large grain formation in rice. THE NEW PHYTOLOGIST 2024; 243:2251-2264. [PMID: 39073105 DOI: 10.1111/nph.20001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 07/05/2024] [Indexed: 07/30/2024]
Abstract
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.
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Affiliation(s)
- Fengcheng Li
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Lian Wu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiang Li
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Yanan Chai
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Nan Ruan
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Ye Wang
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Na Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhiwen Yu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaoche Wang
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Hao Chen
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Jiahao Lu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Hai Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenfu Chen
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
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Xu N, Qiu Y, Cui X, Fei C, Xu Q. Enhancing grain shape, thermotolerance, and alkaline tolerance via Gγ protein manipulation in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:154. [PMID: 38856926 DOI: 10.1007/s00122-024-04669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/01/2024] [Indexed: 06/11/2024]
Abstract
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.
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Affiliation(s)
- Na Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuchao Qiu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Cui
- Key Laboratory of Biochar and Soil Improvement, Ministry of Agriculture and Rural Affairs, Shenyang Agricultural University, Shenyang, 110866, China
| | - Cheng Fei
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China.
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China.
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3
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Ma Q, Liu HS, Li HJ, Bai WP, Gao QF, Wu SD, Yin XX, Chen QQ, Shi YQ, Gao TG, Bao AK, Yin HJ, Li L, Rowland O, Hepworth SR, Luan S, Wang SM. Genomic analysis reveals phylogeny of Zygophyllales and mechanism for water retention of a succulent xerophyte. PLANT PHYSIOLOGY 2024; 195:617-639. [PMID: 38285060 DOI: 10.1093/plphys/kiae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
Revealing the genetic basis for stress-resistant traits in extremophile plants will yield important information for crop improvement. Zygophyllum xanthoxylum, an extant species of the ancient Mediterranean, is a succulent xerophyte that can maintain a favorable water status under desert habitats; however, the genetic basis of this adaptive trait is poorly understood. Furthermore, the phylogenetic position of Zygophyllales, to which Z. xanthoxylum belongs, remains controversial. In this study, we sequenced and assembled the chromosome-level genome of Z. xanthoxylum. Phylogenetic analysis showed that Zygophyllales and Myrtales form a separated taxon as a sister to the clade comprising fabids and malvids, clarifying the phylogenetic position of Zygophyllales at whole-genome scale. Analysis of genomic and transcriptomic data revealed multiple critical mechanisms underlying the efficient osmotic adjustment using Na+ and K+ as "cheap" osmolytes that Z. xanthoxylum has evolved through the expansion and synchronized expression of genes encoding key transporters/channels and their regulators involved in Na+/K+ uptake, transport, and compartmentation. It is worth noting that ZxCNGC1;1 (cyclic nucleotide-gated channels) and ZxCNGC1;2 constituted a previously undiscovered energy-saving pathway for Na+ uptake. Meanwhile, the core genes involved in biosynthesis of cuticular wax also featured an expansion and upregulated expression, contributing to the water retention capacity of Z. xanthoxylum under desert environments. Overall, these findings boost the understanding of evolutionary relationships of eudicots, illustrate the unique water retention mechanism in the succulent xerophyte that is distinct from glycophyte, and thus provide valuable genetic resources for the improvement of stress tolerance in crops and insights into the remediation of sodic lands.
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Affiliation(s)
- Qing Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hai-Shuang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hu-Jun Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wan-Peng Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Qi-Fei Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Sheng-Dan Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Xiu-Xia Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Qin-Qin Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ya-Qi Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Tian-Ge Gao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ai-Ke Bao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hong-Ju Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Li Li
- Institute of Grassland, Xinjiang Academy of Animal Science, Urumqi 830000, China
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Suo-Min Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (BETHESDA, MD.) 2023; 13:jkad174. [PMID: 37535690 PMCID: PMC10542218 DOI: 10.1093/g3journal/jkad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
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Affiliation(s)
| | | | - Philippe Cubry
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
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Fang Y, Liu H, Qin L, Qi F, Sun Z, Wu J, Dong W, Huang B, Zhang X. Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.). BMC Genomics 2023; 24:495. [PMID: 37641021 PMCID: PMC10463326 DOI: 10.1186/s12864-023-09568-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Improving its yield is crucial for sustainable peanut production to meet increasing food and industrial requirements. Deciphering the genetic control underlying peanut kernel weight and size, which are essential components of peanut yield, would facilitate high-yield breeding. A high-density single nucleotide polymorphism (SNP)-based linkage map was constructed using a recombinant inbred lines (RIL) population derived from a cross between the variety Yuanza9102 and a germplasm accession wt09-0023. Kernel weight and size quantitative trait loci (QTLs) were co-localized to a 0.16 Mb interval on Arahy07 using inclusive composite interval mapping (ICIM). Analysis of SNP, and Insertion or Deletion (INDEL) markers in the QTL interval revealed a gene encoding a pentatricopeptide repeat (PPR) superfamily protein as a candidate closely linked with kernel weight and size in cultivated peanut. Examination of the PPR gene family indicated a high degree of collinearity of PPR genes between A. hypogaea and its diploid progenitors, Arachis duranensis and Arachis ipaensis. The candidate PPR gene, Arahy.JX1V6X, displayed a constitutive expression pattern in developing seeds. These findings lay a foundation for further fine mapping of QTLs related to kernel weight and size, as well as validation of candidate genes in cultivated peanut.
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Affiliation(s)
- Yuanjin Fang
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Hua Liu
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Li Qin
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Feiyan Qi
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Ziqi Sun
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jihua Wu
- Shangqiu Academy of Agriculture and Forestry, Shangqiu, 476002, China
| | - Wenzhao Dong
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Bingyan Huang
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China.
| | - Xinyou Zhang
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
- Henan Academy of Agricultural Sciences/Henan Institute of Crop Molecular Breeding/Shennong Laboratory/Key Laboratory of Oil Crops in Huang-Huai-Hai Planis, Ministry of Agriculture and Rural Affairs/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China.
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Pan YH, Nong BX, Chen L, Yang XH, Xia XZ, Zhang ZQ, Qing DJ, Gao J, Huang CC, Li DT, Deng GF. QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice. Genes Genomics 2023; 45:867-885. [PMID: 37209287 DOI: 10.1007/s13258-023-01394-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/01/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Cold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe. OBJECTIVE This study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment. METHODS A chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage. RESULTS A high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11. CONCLUSIONS This study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.
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Affiliation(s)
- Ying-Hua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Bao-Xuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Lei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xing-Hai Yang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Xiu-Zhong Xia
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zong-Qiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Dong-Jin Qing
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Ju Gao
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Cheng-Cui Huang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Dan-Ting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Guo-Fu Deng
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
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Wang H, Zhu Y, Wang L, Xiao C, Yuan J, Liu YG, Zhang Q. Double Mutation of Days to Heading 2 and CONSTANS 3 Improves Agronomic Performance of Japonica Rice under Short Daylight Conditions in Southern China. Int J Mol Sci 2023; 24:ijms24087346. [PMID: 37108508 PMCID: PMC10138775 DOI: 10.3390/ijms24087346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/05/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Some progress has been made in understanding the pathways related to rice heading, but their applications to breeding japonica rice varieties adapted to grow in low-latitude areas ("indica to japonica") are limited. We edited eight adaptation-related genes via a lab-established CRISPR/Cas9 system in a japonica variety, Shennong265 (SN265). All T0 plants and their progeny bearing random mutation permutations were planted in southern China and screened for changes in heading date. We found that the double mutant of Days to heading 2 (DTH2) and CONSTANS 3 (OsCO3) (dth2-osco3), two CONSTANS-like (COL) genes, showed significantly delayed heading under both short-day (SD) and long-day (LD) conditions in Guangzhou and manifested great yield increase under SD conditions. We further demonstrated that the heading-related Hd3a-OsMADS14 pathway was down-regulated in the dth2-osco3 mutant lines. The editing of the COL genes DTH2 and OsCO3 greatly improves the agronomic performance of japonica rice in Southern China.
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Affiliation(s)
- Hongmei Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yue Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Linlin Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Chujian Xiao
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jianming Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yao-Guang Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qunyu Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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8
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Jiang S, Zhang X, Yang X, Liu C, Wang L, Ma B, Miao Y, Hu J, Tan K, Wang Y, Jiang H, Wang J. 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. FRONTIERS IN PLANT SCIENCE 2023; 14:1134308. [PMID: 36909446 PMCID: PMC9995481 DOI: 10.3389/fpls.2023.1134308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
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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Affiliation(s)
- Shukun Jiang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Xijuan Zhang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xianli Yang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chuanzeng Liu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Lizhi Wang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Bo Ma
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Yi Miao
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Jifang Hu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Kefei Tan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Yuxian Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Hui Jiang
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Junhe Wang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
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9
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Liu X, Deng X, Kong W, Sun T, Li Y. The Pyramiding of Elite Allelic Genes Related to Grain Number Increases Grain Number per Panicle Using the Recombinant Lines Derived from Indica-japonica Cross in Rice. Int J Mol Sci 2023; 24:ijms24021653. [PMID: 36675168 PMCID: PMC9865901 DOI: 10.3390/ijms24021653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Indica(xian)-japonica(geng) hybrid rice has many heterosis traits that can improve rice yield. However, the traditional hybrid technology will struggle to meet future needs for the development of higher-yield rice. Available genomics resources can be used to efficiently understand the gene-trait association trait for rice breeding. Based on the previously constructed high-density genetic map of 272 high-generation recombinant inbred lines (RILs) originating from the cross of Luohui 9 (indica, as female) and RPY geng (japonica, as male) and high-quality genomes of parents, here, we further explore the genetic basis for an important complex trait: possible causes of grain number per panicle (GNPP). A total of 20 genes related to grains number per panicle (GNPP) with the differences of protein amino acid between LH9 and RPY were used to analyze genotype combinations, and PCA results showed a combination of PLY1, LAX1, DTH8 and OSH1 from the RPY geng with PYL4, SP1, DST and GNP1 from Luohui 9 increases GNPP. In addition, we also found that the combination of LAX1-T2 and GNP1-T3 had the most significant increase in GNPP. Notably, Molecular Breeding Knowledgebase (MBK) showed a few aggregated rice cultivars, LAX1-T2 and GNP1-T3, which may be a result of the natural geographic isolation between the two gene haplotypes. Therefore, we speculate that the pyramiding of japonica-type LAX-T2 with indica-type GNP1-T3 via hybridization can significantly improve rice yield by increasing GNPP.
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Affiliation(s)
- Xuhui Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Weilong Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence:
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10
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Wang Y, Li F, Zhang F, Wu L, Xu N, Sun Q, Chen H, Yu Z, Lu J, Jiang K, Wang X, Wen S, Zhou Y, Zhao H, Jiang Q, Wang J, Jia R, Sun J, Tang L, Xu H, Hu W, Xu Z, Chen W, Guo A, Xu Q. Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:202-218. [PMID: 36196761 PMCID: PMC9829401 DOI: 10.1111/pbi.13938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/23/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Temperate japonica/geng (GJ) rice yield has significantly improved due to intensive breeding efforts, dramatically enhancing global food security. However, little is known about the underlying genomic structural variations (SVs) responsible for this improvement. We compared 58 long-read assemblies comprising cultivated and wild rice species in the present study, revealing 156 319 SVs. The phylogenomic analysis based on the SV dataset detected the putatively selected region of GJ sub-populations. A significant portion of the detected SVs overlapped with genic regions were found to influence the expression of involved genes inside GJ assemblies. Integrating the SVs and causal genetic variants underlying agronomic traits into the analysis enables the precise identification of breeding signatures resulting from complex breeding histories aimed at stress tolerance, yield potential and quality improvement. Further, the results demonstrated genomic and genetic evidence that the SV in the promoter of LTG1 is accounting for chilling sensitivity, and the increased copy numbers of GNP1 were associated with positive effects on grain number. In summary, the current study provides genomic resources for retracing the properties of SVs-shaped agronomic traits during previous breeding procedures, which will assist future genetic, genomic and breeding research on rice.
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Affiliation(s)
- Yu Wang
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Fengcheng Li
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Fan Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Lian Wu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Na Xu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Qi Sun
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Hao Chen
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Zhiwen Yu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Jiahao Lu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Kai Jiang
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Xiaoche Wang
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Siyu Wen
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Yao Zhou
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Hui Zhao
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Qian Jiang
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | | | - Ruizong Jia
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Jian Sun
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Liang Tang
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Hai Xu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Wei Hu
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Wenfu Chen
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
| | - Anping Guo
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction Regions, Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural UniversityShenyangChina
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11
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Kong W, Deng X, Liao Z, Wang Y, Zhou M, Wang Z, Li Y. De novo assembly of two chromosome-level rice genomes and bin-based QTL mapping reveal genetic diversity of grain weight trait in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:995634. [PMID: 36072319 PMCID: PMC9443666 DOI: 10.3389/fpls.2022.995634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Following the "green revolution," indica and japonica hybrid breeding has been recognized as a new breakthrough in further improving rice yields. However, heterosis-related grain weight QTLs and the basis of yield advantage among subspecies has not been well elucidated. We herein de novo assembled the chromosome level genomes of an indica/xian rice (Luohui 9) and a japonica/geng rice (RPY geng) and found that gene number differences and structural variations between these two genomes contribute to the differences in agronomic traits and also provide two different favorable allele pools to produce better derived recombinant inbred lines (RILs). In addition, we generated a high-generation (> F15) population of 272 RILs from the cross between Luohui 9 and RPY geng and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA, indica and Z7A, japonica). Based on three derived populations, we totally identified eight 1,000-grain weight (KGW) QTLs and eight KGW heterosis loci. Of QTLs, qKGW-6.1 and qKGW-8.1 were accepted as novel KGW QTLs that have not been reported previously. Interestingly, allele genotyping results revealed that heading date related gene (Ghd8) in qKGW-8.1 and qLH-KGW-8.1, can affect grain weight in RILs and rice core accessions and may also play an important role in grain weight heterosis. Our results provided two high-quality genomes and novel gene editing targets for grain weight for future rice yield improvement project.
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Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhenyang Liao
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yibin Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingao Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhaohai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the People’s Republic of China, Nanchang, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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12
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Wang M, Chen J, Zhou F, Yuan J, Chen L, Wu R, Liu Y, Zhang Q. The ties of brotherhood between japonica and indica rice for regional adaptation. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1369-1379. [PMID: 34902099 DOI: 10.1007/s11427-021-2019-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Selection of beneficial genomic variants was crucial for regional adaptation of crops during domestication, but the underlying genomic basis remains largely unexplored. Here we report a genome-wide selective-sweep analysis of 655 japonica and 1,205 indica accessions selected from 2,673 landraces through principal component analysis to identify 5,636 non-synonymous single nucleotide polymorphisms (SNPs) fixed in at least one subspecies. We classified these SNPs into three groups, jiS (japonica- and indica-selected), jS (japonica-selected only), and iS (indica-selected only), and documented evidence for selection acting on these groups, their relation to yield-related traits, such as heading date, and their practical value in cropping area prediction. We also demonstrated the role of a jiS-SNP-containing gene in temperature adaptability. Our study informs genes underpinning adaptation that may shape Green Super Rice and proposes a time-saving, cost-reducing selection strategy of genomic breeding, sweep-SNP-guided selection, for developing regionally-adapted heterosis.
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Affiliation(s)
- Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jiehu Chen
- Science Corporation of Gene, Guangzhou, 510000, China
| | - Feng Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jianming Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Libin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Rongling Wu
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- SCAU Main Campus Teaching & Research Base, Guangzhou, 510642, China.
| | - Qunyu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- SCAU Main Campus Teaching & Research Base, Guangzhou, 510642, China.
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13
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Kong W, Deng X, Yang J, Zhang C, Sun T, Ji W, Zhong H, Fu X, Li Y. High-resolution bin-based linkage mapping uncovers the genetic architecture and heterosis-related loci of plant height in indica-japonica derived populations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:814-827. [PMID: 35165965 DOI: 10.1111/tpj.15705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH-related genes must be urgently identified to facilitate ideal plant architecture breeding in rice (Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis-related loci of PH in rice, we developed a high-generation (>F15 ) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA [indica] and Z7A [japonica]). Using deep resequencing data, a high-density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH-related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment-specific PH QTLs were stably detected in Hainan (qPH-3.1) or Hubei (qPH-5.1), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine-mapped, and the candidate genes qPH-3.1 and qPH-5.1 for PH were further validated using CRISPR-Cas9 gene editing. Specifically, qPH-3.1 was characterized as a pleiotropic gene, and the qPH-3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis-related QTLs were identified in the testcross populations, and a better-parent heterosis locus (qBPH-5.2) completely covered qPH-5.1. Furthermore, the cross results of fixed-genotype RILs verified the dominant effects of qPH-3.1 and qPH-5.1. Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future.
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Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wenjie Ji
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hua Zhong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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14
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Genome sequencing and genetic analysis of recombinant inbred lines reveals important agronomic traits related loci under different nitrogen fertilization. Mol Biol Rep 2022; 49:4545-4553. [PMID: 35262821 DOI: 10.1007/s11033-022-07298-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/23/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND The intensive application of inorganic nitrogen has contributed to increasing the crop yield with the risk of environmental damage. High nitrogen fertilizer requirements are a long-standing problem in japonica cultivation. MATERIALS AND METHODS In the present study, 200 recombinant inbred lines derived from two representative japonica varieties of Japanese and Chinese varieties, Akitakomachi and Liaogeng5, respectively, were planted under different nitrogen fertilization conditions. The relationships among nitrogen fertilization, genetic background, and important agronomic traits were surveyed through the phenotypic investigation and next-generation sequencing. RESULTS The results showed that the yield components of Akitakomachi dramatically decreased along with the nitrogen reduction, whereas those of Liaogeng5 exhibited a slight decrease. The appearance quality and milling quality of both Akitakomachi and Liaogeng5 were improved, especially Liaogeng5. The recombinant inbred lines (RILs) showed similar trends to their parental lines. The QTLs analysis of important agronomic traits detected 17 loci, one QTL clustering located on chromosome 9 that corresponded to the plant height, panicle angle, grain number per panicle, harvest index, and taste value was identified to be synonymous with a previously reported gene, DEP1. The function of DEP1 was verified by a knock-out mutant constructed by CRISPR/Cas9. The dep1 mutant exhibited improved grain quality without severe yield penalty under nitrogen reduction conditions. CONCLUSION The results of the present study provide useful information for the improvement of food security by enhancing nitrogen use efficiency.
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15
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Deng X, Kong W, Sun T, Zhang C, Zhong H, Zhao G, Liu X, Qiang Y, Li Y. Bin mapping-based QTL analyses using three genetic populations derived from indica-japonica crosses uncover multiple grain shape heterosis-related loci in rice. THE PLANT GENOME 2022; 15:e20171. [PMID: 34806841 DOI: 10.1002/tpg2.20171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Exploitation of heterosis between indica and japonica has important significance in scientific research and agriculture application. However, the molecular mechanism of grain shape heterosis in indica-japonica hybrid remains unknown in rice (Oryza sativa L.). To reveal the genetic mechanism of grain shape in indica--japonica hybrid, we constructed a high-generation recombinant inbred line (RIL) population and two testcross hybrid populations derived from the cross of RILs and two cytoplasmic male sterile material (YTA and Z7A) and then performed a bin mapping-based quantitative trait locus (QTL) mapping of multiple grain shape traits, such as grain length (GL), grain width (GW), and grain length-to-width ratio (GLWR). A total of sixteen QTLs and 30 heterosis-related QTLs of grain shape traits were detected. We found that GS3, GS5, and OsPPKL2 were also correlated with grain shape both in RILs and two testcross hybrid populations. Homologous gene analysis emphasized two candidate grain shape-associated genes (LOC_Os06g14260 and LOC_Os04g51950). Our findings uncover multiple grain shape heterosis-related loci and provides a new insight into heterosis mechanism of grain shape in rice.
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Affiliation(s)
- Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Hua Zhong
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Gangqing Zhao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Xuhui Liu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Yalin Qiang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
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16
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Pezzotti G, Zhu W, Hashimoto Y, Marin E, Masumura T, Sato YI, Nakazaki T. Raman Fingerprints of Rice Nutritional Quality: A Comparison between Japanese Koshihikari and Internationally Renowned Cultivars. Foods 2021; 10:foods10122936. [PMID: 34945487 PMCID: PMC8701134 DOI: 10.3390/foods10122936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Raman spectroscopy was applied to characterize at the molecular scale the nutritional quality of the Japanese Koshihikari rice cultivar in comparison with other renowned rice cultivars including Carnaroli from Italy, Calrose from the USA, Jasmine rice from Thailand, and Basmati from both India and Pakistan. For comparison, two glutinous (mochigome) cultivars were also investigated. Calibrated and validated Raman analytical algorithms allowed quantitative determinations of: (i) amylopectin and amylose concentrations, (ii) fractions of aromatic amino acids, and (iii) protein content and secondary structure. The Raman assessments non-destructively linked the molecular composition of grains to key nutritional parameters and revealed a complex intertwine of chemical properties. The Koshihikari cultivar was rich in proteins (but with low statistical relevance as compared to other investigated cultivars) and aromatic amino acids. However, it also induced a clearly higher glycemic impact as compared to long-grain cultivars from Asian countries. Complementary to genomics and wet-chemistry analyses, Raman spectroscopy makes non-destructively available factual and data-driven information on rice nutritional characteristics, thus providing customers, dietitian nutritionists, and producers with a solid science-consolidated platform.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (W.Z.); tennis-0319-@outlook.com (Y.H.); (E.M.)
- Department of Orthopedic Surgery, Tokyo Medical University, 6-7-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 160-0023, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, 2-2 Yamadaoka, Suita 565-0854, Japan
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, 465 Kajii-cho, Kyoto 602-8566, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Correspondence:
| | - Wenliang Zhu
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (W.Z.); tennis-0319-@outlook.com (Y.H.); (E.M.)
| | - Yuuki Hashimoto
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (W.Z.); tennis-0319-@outlook.com (Y.H.); (E.M.)
| | - Elia Marin
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; (W.Z.); tennis-0319-@outlook.com (Y.H.); (E.M.)
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takehiro Masumura
- Laboratory of Genetic Engineering, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan;
| | - Yo-Ichiro Sato
- Research Center for Japanese Food Culture, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-8522, Japan;
| | - Tetsuya Nakazaki
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa 619-0218, Japan;
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Li F, Han Z, Qiao W, Wang J, Song Y, Cui Y, Li J, Ge J, Lou D, Fan W, Li D, Nong B, Zhang Z, Cheng Y, Zhang L, Zheng X, Yang Q. High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:775051. [PMID: 34868173 PMCID: PMC8639688 DOI: 10.3389/fpls.2021.775051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.
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Affiliation(s)
- Fei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenyun Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junrui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Yue Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxia Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jiaqi Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Little Berry Research Room, Liaoning Institute of Fruit Science, Yingkou, China
| | - Jinyue Ge
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danjing Lou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiya Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunlian Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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18
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Pazhamala LT, Kudapa H, Weckwerth W, Millar AH, Varshney RK. Systems biology for crop improvement. THE PLANT GENOME 2021; 14:e20098. [PMID: 33949787 DOI: 10.1002/tpg2.20098] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/09/2021] [Indexed: 05/19/2023]
Abstract
In recent years, generation of large-scale data from genome, transcriptome, proteome, metabolome, epigenome, and others, has become routine in several plant species. Most of these datasets in different crop species, however, were studied independently and as a result, full insight could not be gained on the molecular basis of complex traits and biological networks. A systems biology approach involving integration of multiple omics data, modeling, and prediction of the cellular functions is required to understand the flow of biological information that underlies complex traits. In this context, systems biology with multiomics data integration is crucial and allows a holistic understanding of the dynamic system with the different levels of biological organization interacting with external environment for a phenotypic expression. Here, we present recent progress made in the area of various omics studies-integrative and systems biology approaches with a special focus on application to crop improvement. We have also discussed the challenges and opportunities in multiomics data integration, modeling, and understanding of the biology of complex traits underpinning yield and stress tolerance in major cereals and legumes.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology and School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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19
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Tappiban P, Ying Y, Xu F, Bao J. Proteomics and Post-Translational Modifications of Starch Biosynthesis-Related Proteins in Developing Seeds of Rice. Int J Mol Sci 2021; 22:5901. [PMID: 34072759 PMCID: PMC8199009 DOI: 10.3390/ijms22115901] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Rice (Oryza sativa L.) is a foremost staple food for approximately half the world's population. The components of rice starch, amylose, and amylopectin are synthesized by a series of enzymes, which are responsible for rice starch properties and functionality, and then affect rice cooking and eating quality. Recently, proteomics technology has been applied to the establishment of the differentially expressed starch biosynthesis-related proteins and the identification of posttranslational modifications (PTMs) target starch biosynthesis proteins as well. It is necessary to summarize the recent studies in proteomics and PTMs in rice endosperm to deepen our understanding of starch biosynthesis protein expression and regulation, which will provide useful information to rice breeding programs and industrial starch applications. The review provides a comprehensive summary of proteins and PTMs involved in starch biosynthesis based on proteomic studies of rice developing seeds. Starch biosynthesis proteins in rice seeds were differentially expressed in the developing seeds at different developmental stages. All the proteins involving in starch biosynthesis were identified using proteomics methods. Most starch biosynthesis-related proteins are basically increased at 6-20 days after flowering (DAF) and decreased upon the high-temperature conditions. A total of 10, 14, 2, 17, and 7 starch biosynthesis related proteins were identified to be targeted by phosphorylation, lysine acetylation, succinylation, lysine 2-hydroxyisobutyrylation, and malonylation, respectively. The phosphoglucomutase is commonly targeted by five PTMs types. Research on the function of phosphorylation in multiple enzyme complex formation in endosperm starch biosynthesis is underway, while the functions of other PTMs in starch biosynthesis are necessary to be conducted in the near future.
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Affiliation(s)
- Piengtawan Tappiban
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Yining Ying
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Feifei Xu
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
| | - Jinsong Bao
- Key Laboratory of Nuclear Agricultural Sciences of Ministry of Agriculture and Zhejiang Province, Institute of Nuclear Agricultural Sciences, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China; (P.T.); (Y.Y.); (F.X.)
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
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20
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Cui Y, Xu Z, Xu Q. Elucidation of the relationship between yield and heading date using CRISPR/Cas9 system-induced mutation in the flowering pathway across a large latitudinal gradient. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:23. [PMID: 37309418 PMCID: PMC10236111 DOI: 10.1007/s11032-021-01213-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/03/2021] [Indexed: 06/14/2023]
Abstract
The naturally occurring genetic variation in the universal flowering (or heading date in crops) pathway has produced major advancements in crop domestication and expansion, and the various combinations of heading date genes have facilitated the plants to heading at suitable times in different ecological zones. However, gene combinations that can maximize crop yields may not exist in natural populations. Here, we planted a series of heading date mutants that harbored different heading mutant gene combinations generated by CRISPR/Cas9 gene editing technology, along with a collection of commercial varieties, across a large latitude gradient to evaluate the major effects of heading date genes and preferable gene combinations for each area. The relationship between yield and heading date was investigated. According to the pattern obtained from gene editing mutants, we concluded that the growth period of commercial varieties could be adjusted to achieve maximum yield performance in some areas. By combining the long vegetative growth allele and weak photoperiod sensitivity allele, we pinpointed an optimal balance between growth period and yield production, resulting in new partially determinate heading date to maximum yields and improved adaptability. We propose that harnessing mutations in the florigen pathway to customize the balance between vegetative and reproductive growth offers a broad toolkit for boosting crop productivity. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01213-4.
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Affiliation(s)
- Yue Cui
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866 China
| | - Zhengjin Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866 China
| | - Quan Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866 China
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21
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Gu Q, Ke H, Liu Z, Lv X, Sun Z, Zhang M, Chen L, Yang J, Zhang Y, Wu L, Li Z, Wu J, Wang G, Meng C, Zhang G, Wang X, Ma Z. A high-density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for fibre quality and yield in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3395-3408. [PMID: 32894321 DOI: 10.1007/s00122-020-03676-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/21/2020] [Indexed: 05/18/2023]
Abstract
A high-density linkage map of an intraspecific RIL population was constructed using 6187 bins to identify QTLs for fibre quality- and yield-related traits in upland cotton by whole-genome resequencing. Good fibre quality and high yield are important production goals in cotton (Gossypium hirsutum L.), which is a leading natural fibre crop worldwide. However, a greater understanding of the genetic variants underlying fibre quality- and yield-related traits is still required. In this study, a large-scale population including 588 F7 recombinant inbred lines, derived from an intraspecific cross between the upland cotton cv. Nongdamian13, which exhibits high quality, and Nongda601, which exhibits a high yield, was genotyped by using 232,946 polymorphic single-nucleotide polymorphisms obtained via a whole-genome resequencing strategy with 4.3-fold genome coverage. We constructed a high-density bin linkage map containing 6187 bin markers spanning 4478.98 cM with an average distance of 0.72 cM. We identified 58 individual quantitative trait loci (QTLs) and 25 QTL clusters harbouring 94 QTLs, and 119 previously undescribed QTLs controlling 13 fibre quality and yield traits across eight environments. Importantly, the QTL counts for fibre quality in the Dt subgenome were more than two times that in the At subgenome, and chromosome D02 harboured the greatest number of QTLs and clusters. Furthermore, we discovered 24 stable QTLs for fibre quality and 12 stable QTLs for yield traits. Four novel major stable QTLs related to fibre length, fibre strength and lint percentage, and seven previously unreported candidate genes with significantly differential expression between the two parents were identified and validated by RNA-seq. Our research provides valuable information for improving the fibre quality and yield in cotton breeding.
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Affiliation(s)
- Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Xing Lv
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Man Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Liting Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Zhikun Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Jinhua Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China.
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, 071001, China.
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22
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Xu X, Li X, Li Z, Li Y, Chen K, Wu L, Fa Y, Xu Z, Xu Q. Effects of Genetic Background and Environmental Conditions on Amylopectin Chain-Length Distribution in a Recombinant Inbred Line of an Inter-subspecies Rice Cross. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:7444-7452. [PMID: 32551583 DOI: 10.1021/acs.jafc.0c02713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Amylopectin is an essential starch property, and the chain-length distribution of amylopectin (APCLD) is closely associated with the eating and cooking quality of rice. In this study, a series of recombinant inbred lines derived from an indica/japonica cross were planted in four areas with distinct ecological conditions (LN, SC, JS, and GD), and the relationship among APCLD, environmental factors, and genetic background was analyzed. The results showed that APCLD was strongly influenced by environmental factors, which dynamically changed from heading to the mature stage. The solar radiation, luminous flux, and light hours were positively correlated with Fa but negatively correlated with Fb1 and Fb2. The temperature was negatively correlated with Fa and Fb1 but positively correlated with Fb2 and Fb3. The temperature was the primary factor affecting APCLD, followed by humidity and light. There was no significant correlation between the indica pedigree percentage and APCLD. Furthermore, we detected six quantitative trait loci related to Fa, Fb1, Fb2, and Fb3 chains, several of which shared a similar region to previously reported loci, including DENSE AND ERECT PANICLE 1 (DEP1). The truncated dep1 allele increased Fa, Fb2, and Fb3 but decreased Fb1 in LN, whereas Fa was decreased but Fb1 and Fb2 were increased in JS. Elucidating the effects of climate factors and genetic background on APCLD could provide a theoretical basis and technical guidance for high-quality rice breeding.
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Affiliation(s)
- Ximing Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Xiukun Li
- Rice Research Institute of Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
- College of Agronomy Qingdao Agricultural University, Qingdao, Shandong 266109, People's Republic of China
| | - Zhibin Li
- Rice Research Institute of Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Yang Li
- Key Laboratory of Southwest Rice Biology and Genetic Breeding, Ministry of Agriculture, Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Deyang, Sichuan 618000, People's Republic of China
| | - Kai Chen
- Agricultural Genomics in Statute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, People's Republic of China
| | - Lian Wu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Yun Fa
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, People's Republic of China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China
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23
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Zhu D, Li X, Wang Z, You C, Nie X, Sun J, Zhang X, Zhang D, Lin Z. Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton. BMC Genomics 2020; 21:431. [PMID: 32586283 PMCID: PMC7318736 DOI: 10.1186/s12864-020-06800-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 01/07/2023] Open
Abstract
Background The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.
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Affiliation(s)
- De Zhu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ximei Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Key Laboratory of Dryland Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Zhiwei Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Peanut Research Institute, Qingdao, 266109, Shangdong, China
| | - Chunyuan You
- Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, Xinjiang, 832003, China
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Jie Sun
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dawei Zhang
- Institute of Industrial Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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24
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Wu M, Liu H, Lin Y, Chen J, Fu Y, Luo J, Zhang Z, Liang K, Chen S, Wang F. In-Frame and Frame-Shift Editing of the Ehd1 Gene to Develop Japonica Rice With Prolonged Basic Vegetative Growth Periods. FRONTIERS IN PLANT SCIENCE 2020; 11:307. [PMID: 32265960 PMCID: PMC7096585 DOI: 10.3389/fpls.2020.00307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/03/2020] [Indexed: 05/05/2023]
Abstract
Japonica rice has become increasingly popular in China owing to its superior grain quality. Over the past decades, "indica to japonica" projects have been proposed to promote cultivation of japonica rice in low latitudes in China. Traditionally, japonica varieties were planted mainly in mid latitudes in the northeast plain and Yangtze River region. The key obstacle for introducing elite mid-latitude japonica varieties to low latitudes is the severe shortening of growth period of the japonica varieties due to their sensitivity to low-latitude short photoperiod and high temperature. Here we report development of new japonica rice with prolonged basic vegetative growth (BVG) periods for low latitudes by targeted editing the Early heading date 1 (Ehd1) gene. Using CRISPR/Cas9 system, we generated both frame-shift and/or in-frame deletion mutants in four japonica varieties, Nipponbare, Longdao16, Longdao24, and Xiushui134. When planting at low-latitude stations, the frame-shift homozygous lines exhibited significantly longer BVG periods compared with wild-types. Interestingly, we observed that minor deletion of the first few residues within the receiver domain could quantitatively impair the function of Ehd1 on activation of Hd3a and RFT1, resulting in an intermediate-long BVG period phenotype in the homozygous in-frame deletion ehd1 lines. Field investigation further showed that, both the in-frame and frame-shift lines exhibited significantly improved yield potential compared with wild-types. Our study demonstrates an effective approach to rapid breeding of elite japonica varieties with intermediate-long and long BVG periods for flexible cropping systems in diverse areas or under different seasons in southern China, and other low-latitude regions.
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Affiliation(s)
- Mingji Wu
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Huaqing Liu
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yan Lin
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianmin Chen
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yanping Fu
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jiami Luo
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Zhujian Zhang
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Kangjing Liang
- College of Agriculture, Fujian Agricultural and Forestry University, Fuzhou, China
| | - Songbiao Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Feng Wang
- Fujian Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
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25
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Cui Y, Jiang N, Xu Z, Xu Q. Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice. BMC PLANT BIOLOGY 2020; 20:90. [PMID: 32111163 PMCID: PMC7048073 DOI: 10.1186/s12870-020-2289-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/13/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The heterotrimeric G protein complex, consisting of Gα, Gβ, and Gγ subunits, are conserved signal transduction mechanism in eukaryotes. Recent molecular researches had demonstrated that G protein signaling participates in the regulation of yield related traits. However, the effects of G protein genes on yield components and stress tolerance are not well characterized. RESULTS In this study, we generated heterotrimeric G protein mutants in rice using CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology. The effects of heterotrimeric G proteins on the regulation of yield components and stress tolerance were investigated. The mutants of gs3 and dep1 generated preferable agronomic traits compared to the wild-type, whereas the mutants of rga1 showed an extreme dwarf phenotype, which led to a dramatic decrease in grain production. The mutants showed improved stress tolerance, especially under salinity treatment. We found four putative extra-large G proteins (PXLG)1-4 that also participate in the regulation of yield components and stress tolerance. A yeast two hybrid showed that the RGB1 might interact with PXLG2 but not with PXLG1, PXLG3 or PXLG4. CONCLUSION These findings will not only improve our understanding of the repertoire of heterotrimeric G proteins in rice but also contribute to the application of heterotrimeric G proteins in rice breeding.
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Affiliation(s)
- Yue Cui
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866 China
| | - Nan Jiang
- Shenyang Research and Development Service Center of Modern Agriculture, Shenyang, 110866 China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866 China
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866 China
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Yu Y, Zhu M, Cui Y, Liu Y, Li Z, Jiang N, Xu Z, Xu Q, Sui G. Genome Sequence and QTL Analyses Using Backcross Recombinant Inbred Lines (BILs) and BILF 1 Lines Uncover Multiple Heterosis-related Loci. Int J Mol Sci 2020; 21:ijms21030780. [PMID: 31991733 PMCID: PMC7038202 DOI: 10.3390/ijms21030780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 01/19/2023] Open
Abstract
: Heterosis is an interesting topic for both breeders and biologists due to its practical importance and scientific significance. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica, and hybrid rice is the predominant form of indica rice in China. However, the molecular mechanism underlying heterosis in japonica remains unclear. The present study determined the genome sequence and conducted quantitative trait locus (QTL) analysis using backcross recombinant inbred lines (BILs) and BILF1 lines to uncover the heterosis-related loci for rice yield increase under a japonica genetic background. The BIL population was derived from an admixture variety Habataki and japonica variety Sasanishiki cross to improve the genetic diversity but maintain the genetic background close to japonica. The results showed that heterosis in F1 mainly involved grain number per panicle. The BILF1s showed an increase in grain number per panicle but a decrease in plant height compared with the BILs. Genetic analysis then identified eight QTLs for heterosis in the BILF1s; four QTLs were detected exclusively in the BILF1 population only, presenting a mode of dominance or super-dominance in the heterozygotes. An additional four loci overlapped with QTLs detected in the BIL population, and we found that Grains Height Date 7 (Ghd7) was correlated in days to heading in both BILs and BILF1s. The admixture genetic background of Habataki was also determined by subspecies-specific single nucleotide polymorphisms (SNPs). This investigation highlights the importance of high-throughput sequencing to elucidate the molecular mechanism of heterosis and provides useful germplasms for the application of heterosis in japonica rice production.
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Affiliation(s)
- Yahui Yu
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China; (Y.Y.)
- Liaoning Institute of Saline-Alkali Land Utilization, Panjin 124010, China
- Liaoning Academy of Agricultural Sciences, Shenyang 110866, China
| | - Mengmeng Zhu
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China; (Y.Y.)
| | - Yue Cui
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China; (Y.Y.)
| | - Yu Liu
- Liaoning Institute of Saline-Alkali Land Utilization, Panjin 124010, China
| | - Zhenyu Li
- Liaoning Institute of Saline-Alkali Land Utilization, Panjin 124010, China
| | - Nan Jiang
- Shenyang Research and Development Service Center of Modern Agriculture, Shenyang 110034, China
| | - Zhengjin Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China; (Y.Y.)
| | - Quan Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China; (Y.Y.)
- Correspondence: (Q.X.); (G.S.)
| | - Guomin Sui
- Liaoning Academy of Agricultural Sciences, Shenyang 110866, China
- Correspondence: (Q.X.); (G.S.)
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Wu L, Cui Y, Xu Z, Xu Q. Identification of Multiple Grain Shape-Related Loci in Rice Using Bulked Segregant Analysis With High-Throughput Sequencing. FRONTIERS IN PLANT SCIENCE 2020; 11:303. [PMID: 32308659 PMCID: PMC7145986 DOI: 10.3389/fpls.2020.00303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/03/2020] [Indexed: 05/17/2023]
Abstract
Grain shape (GS) is an important agronomic trait that can improve rice breeding for optimal appearance quality, and it varies highly between indica and japonica subspecies. In this study, we conducted a genome sequencing of a series of recombination inbred lines (RILs) derived from a cross between japonica variety Shennong265 (SN265) and indica variety R99, and we successfully detected seven loci associated with GS. Subsequent analysis showed that a major quantitative trait locus (QTL) corresponded to the qSW5/GW5. To identify a main-effect locus, we conducted bulked segregant analysis (BSA) in two F2 populations. A 0.8-Mb region on chromosome 9 was identified as the candidate region of GS. There are 101 predicted genes in this region, and eight single nucleotide polymorphisms/insertions and deletions (SNPs/INDELs) caused frameshift. We found that a 637-bp stretch in exon 5 of the DENSE AND ERECT PANICLE 1 (DEP1) locus in SN265 was replaced by a 12-bp sequence. The two types of CRISPR/Cas9 gene-edited plants confirmed that DEP1 affected GS, and both Gγ and Cys-rich domains participated in this regulatory mechanism. These findings improve our understanding of the underlying mechanism of GS in rice and provide an effective and rapid strategy for the identification of main-effect loci of target traits.
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Li Q, Pan Z, Gao Y, Li T, Liang J, Zhang Z, Zhang H, Deng G, Long H, Yu M. Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number. FRONTIERS IN PLANT SCIENCE 2020; 11:600788. [PMID: 33424899 PMCID: PMC7793810 DOI: 10.3389/fpls.2020.600788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/11/2020] [Indexed: 05/14/2023]
Abstract
Numerous quantitative trait loci (QTLs) have been identified for wheat quality; however, most are confined to low-density genetic maps. In this study, based on specific-locus amplified fragment sequencing (SLAF-seq), a high-density genetic map was constructed with 193 recombinant inbred lines derived from Chuanmai 42 and Chuanmai 39. In total, 30 QTLs with phenotypic variance explained (PVE) up to 47.99% were identified for falling number (FN), grain protein content (GPC), grain hardness (GH), and starch pasting properties across three environments. Five NAM genes closely adjacent to QGPC.cib-4A probably have effects on GPC. QGH.cib-5D was the only one detected for GH with high PVE of 33.31-47.99% across the three environments and was assumed to be related to the nearest pina-D1 and pinb-D1genes. Three QTLs were identified for FN in at least two environments, of which QFN.cib-3D had relatively higher PVE of 16.58-25.74%. The positive effect of QFN.cib-3D for high FN was verified in a double-haploid population derived from Chuanmai 42 × Kechengmai 4. The combination of these QTLs has a considerable effect on increasing FN. The transcript levels of Basic 7S globulin and Basic 7S globulin 2 in QFN.cib-3D were significantly different between low FN and high FN bulks, as observed through bulk segregant RNA-seq (BSR). These QTLs and candidate genes based on the high-density genetic map would be beneficial for further understanding of the genetic mechanism of quality traits and molecular breeding of wheat.
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Affiliation(s)
- Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- *Correspondence: Zhifen Pan, ; orcid.org/0000-0002-1692-5425
| | - Yuan Gao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zijin Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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An Y, Mi X, Zhao S, Guo R, Xia X, Liu S, Wei C. Revealing Distinctions in Genetic Diversity and Adaptive Evolution Between Two Varieties of Camellia sinensis by Whole-Genome Resequencing. FRONTIERS IN PLANT SCIENCE 2020; 11:603819. [PMID: 33329675 PMCID: PMC7732639 DOI: 10.3389/fpls.2020.603819] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/03/2020] [Indexed: 05/07/2023]
Abstract
Camellia sinensis var. sinensis (CSS) and C. sinensis var. assamica (CSA) are the two most economically important tea varieties. They have different characteristics and geographical distribution. Their genetic diversity and differentiation are unclear. Here, we identified 18,903,625 single nucleotide polymorphisms (SNPs) and 7,314,133 insertion-deletion mutations (indels) by whole-genome resequencing of 30 cultivated and three wild related species. Population structure and phylogenetic tree analyses divided the cultivated accessions into CSS and CSA containing 6,440,419 and 6,176,510 unique variations, respectively. The CSS subgroup possessed higher genetic diversity and was enriched for rare alleles. The CSA subgroup had more non-synonymous mutations and might have experienced a greater degree of balancing selection. The evolution rate (dN/dS) and KEGG enrichment indicated that genes involved in the synthesis and metabolism of flavor substances were positively selected in both CSS and CSA subpopulations. However, there are extensive genome differentiation regions (2959 bins and approximately 148 M in size) between the two subgroups. Compared with CSA (141 selected regions containing 124 genes), the CSS subgroup (830 selected regions containing 687 genes) displayed more selection regions potentially related to environmental adaptability. Fifty-three pairs of polymorphic indel markers were developed. Some markers were located in hormone-related genes with distinct alleles in the two cultivated subgroups. These identified variations and selected regions provide clues for the differentiation and adaptive evolution of tea varieties. The newly developed indel markers will be valuable in further genetic research on tea plants.
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Rana N, Rahim MS, Kaur G, Bansal R, Kumawat S, Roy J, Deshmukh R, Sonah H, Sharma TR. Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.). Crit Rev Food Sci Nutr 2019; 60:3304-3320. [DOI: 10.1080/10408398.2019.1685454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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31
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Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper ( Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS. Int J Mol Sci 2019; 20:ijms20225675. [PMID: 31766117 PMCID: PMC6888518 DOI: 10.3390/ijms20225675] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022] Open
Abstract
There are many agronomic traits of pepper (Capsicum L.) with abundant phenotypes that can benefit pepper growth. Using specific-locus amplified fragment sequencing (SLAF-seq), a genome-wide association study (GWAS) of 36 agronomic traits was carried out for 287 representative pepper accessions. To ensure the accuracy and reliability of the GWAS results, we analyzed the genetic diversity, distribution of labels (SLAF tags and single nucleotide polymorphisms (SNPs)) and population differentiation and determined the optimal statistical model. In our study, 1487 SNPs were highly significantly associated with 26 agronomic traits, and 2126 candidate genes were detected in the 100-kb region up- and down-stream near these SNPs. Furthermore, 13 major association peaks were identified for 11 key agronomic traits. Then we examined the correlations among the 36 agronomic traits and analyzed SNP distribution and found 37 SNP polymerization regions (total size: 264.69 Mbp) that could be selected areas in pepper breeding. We found that the stronger the correlation between the two traits, the greater the possibility of them being in more than one polymerization region, suggesting that they may be linked or that one pleiotropic gene controls them. These results provide a theoretical foundation for future multi-trait pyramid breeding of pepper. Finally, we found that the GWAS signals were highly consistent with those from the nuclear restorer-of-fertility (Rf) gene for cytoplasmic male sterility (CMS), verifying their reliability. We further identified Capana06g002967 and Capana06g002969 as Rf candidate genes by functional annotation and expression analysis, which provided a reference for the study of cytoplasmic male sterility in Capsicum.
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32
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Misra G, Anacleto R, Badoni S, Butardo V, Molina L, Graner A, Demont M, Morell MK, Sreenivasulu N. Dissecting the genome-wide genetic variants of milling and appearance quality traits in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5115-5130. [PMID: 31145789 PMCID: PMC6793453 DOI: 10.1093/jxb/erz256] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/20/2019] [Indexed: 05/19/2023]
Abstract
Higher head rice yield (HRY), which represents the proportion of intact grains that survive milling, and lower grain chalkiness (opacity) are key quality traits. We investigated the genetic basis of HRY and chalkiness in 320 diverse resequenced accessions of indica rice with integrated single- and multi-locus genome-wide association studies using 2.26 million single-nucleotide polymorphisms. We identified novel haplotypes that underly higher HRY on chromosomes 3, 6, 8, and 11, and that lower grain chalkiness in a fine-mapped region on chromosome 5. Whole-genome sequencing of 92 IRRI breeding lines was performed to identify the genetic variants of HRY and chalkiness. Rare and novel haplotypes were found for lowering chalkiness, but missing alleles hindered progress towards enhancing HRY in breeding material. The novel haplotypes that we identified have potential use in breeding programs aimed at improving these important traits in the rice crop.
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Affiliation(s)
- Gopal Misra
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Roslen Anacleto
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Saurabh Badoni
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Vito Butardo
- International Rice Research Institute, DAPO, Metro Manila, Philippines
- Present address: Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria, Australia
| | - Lilia Molina
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland OT Gatersleben, Germany
| | - Matty Demont
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Matthew K Morell
- International Rice Research Institute, DAPO, Metro Manila, Philippines
| | - Nese Sreenivasulu
- International Rice Research Institute, DAPO, Metro Manila, Philippines
- Correspondence:
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Custodio MC, Cuevas RP, Ynion J, Laborte AG, Velasco ML, Demont M. Rice quality: How is it defined by consumers, industry, food scientists, and geneticists? Trends Food Sci Technol 2019; 92:122-137. [PMID: 31787805 PMCID: PMC6876681 DOI: 10.1016/j.tifs.2019.07.039] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND Quality is a powerful engine in rice value chain upgrading. However, there is no consensus on how "rice quality" should be defined and measured in the rice sector. SCOPE AND APPROACH We adopt a Lancasterian definition of rice quality as a bundle of intrinsic and extrinsic attributes. We then review how rice quality is (i) perceived and defined by consumers and industry stakeholders in rice value chains in Southeast and South Asia; (ii) measured and defined by food technologists; and (iii) predicted through genetics. KEY FINDINGS AND CONCLUSIONS Consumers are heterogeneous with respect to their perceived differentiation of rice quality among regions, countries, cities, and urbanization levels. Premium quality is defined by nutritional benefits, softness and aroma in Southeast Asia, and by the physical appearance of the grains (uniformity, whiteness, slenderness), satiety, and aroma in South Asia. These trends are found to be consistent with industry perceptions and have important implications for regional and national breeding programs in terms of tailoring germplasm to regions and rice varieties to specific local market segments. Because rice is traded internationally, there is a need to standardize definitions of rice quality. However, food technologists have not reached unanimity on quality classes and measurement; routine indicators need to be complemented by descriptive profiles elicited through sensory evaluation panels. Finally, because rice quality is controlled by multiple interacting genes expressed through environmental conditions, predicting grain quality requires associating genetic information with grain quality phenotypes in different environments.
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Cui Y, Zhu M, Xu Z, Xu Q. Assessment of the effect of ten heading time genes on reproductive transition and yield components in rice using a CRISPR/Cas9 system. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1887-1896. [PMID: 30887096 DOI: 10.1007/s00122-019-03324-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/11/2019] [Indexed: 05/22/2023]
Abstract
We demonstrated the effect of heading time genes on reproductive transition and yield components under an identical genetic background using CRISPR/Cas9 gene-editing technology, and we propose that the elite allele will provide a new breeding strategy for rice breeding in high-latitude regions. Heading date is a factor closely associated with grain yield in rice (Oryza sativa L). In recent decades, a number of genes responsible for heading time have been identified, the variation of which contributes to the expansion of the rice cultivation area. However, it is difficult to compare the phenotypic effects of these genes due to the different genetic backgrounds. In this study, we generated 14 heading time mutants using CRISPR/Cas9 gene-editing technology and marker-assisted selection with a japonica Sasanishiki wild-type (WT) genetic background. Photoperiod sensitivity, the relationship between days to heading (DTH), and yield components of mutants were investigated. We found that the yield increases with increases in DTH, but eventually plateaus at maximum and then began to decrease, whereas the biomass continued to increase. The mutants exerted distinctly different effects on DTH and yield components. The convergent double mutants had severe yield reduction compared with single mutants, even with a DTH that was similar to that of single mutants. We also found that an elite mutant of se14 achieved a yield equal to that of the WT, but with heading occurring 10 days earlier. A sequence analysis of 72 cultivars collected from the japonica cultivated zone shows that elite se14 mutants have not been applied to rice breeding. Our study demonstrates the effect of heading time genes on reproductive transition and yield components under an identical genetic background. These results may provide new insights into rice breeding using heading time mutants.
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Affiliation(s)
- Yue Cui
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Mengmeng Zhu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China.
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Xu X, Xu Z, Matsue Y, Xu Q. Effects of Genetic Background and Environmental Conditions on Texture Properties in a Recombinant Inbred Population of an Inter-Subspecies Cross. RICE (NEW YORK, N.Y.) 2019; 12:32. [PMID: 31073677 PMCID: PMC6509310 DOI: 10.1186/s12284-019-0286-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Eating and cooking quality have become ever more important breeding goals due to high levels of economic growth in Asia in recent decades. Cooked rice texture properties such as hardness, stickiness, and springiness are appealing to human mastication and directly reflect eating and cooking quality, and texture is strongly affected by genetic background and environmental conditions. RESULTS In this study, a series of recombinant inbred lines (RILs) derived from an indica/japonica cross were planted into four typical rice-cultivated areas. The relationships between the environment, texture, and genetic background of the RILs were investigated. The results showed that hardness, stickiness, and springiness strongly correlated with amylose and protein contents. Texture was strongly affected by environmental factors, which dynamically changed from the heading to the mature stage. Interestingly, the effect of environmental factors became weaker with decreasing latitude. The hardness and stickiness increased with the decrease of latitude, whereas springiness exhibited the opposite trend. The indica pedigree percentage did not significant correlated with hardness, stickiness and springiness. We detected 19 QTLs related to hardness, stickiness, and springiness, several of which share a similar region with a previously reported locus related to starch synthesis. Moreover, we revealed that DEP1 might affect taste through regulating amylopectin chain length distribution. CONCLUSIONS The present study evaluated the effects of environmental factors and genetic background to texture of cooked rice. These results provide insights into the eating and cooking quality of rice, which can be improved through sub-species crosses for different ecological conditions.
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Affiliation(s)
- Ximing Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuji Matsue
- Kyushu University Global Innovation Center, Fukuoka, 812-8581, Japan.
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China.
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Li R, Li M, Ashraf U, Liu S, Zhang J. Exploring the Relationships Between Yield and Yield-Related Traits for Rice Varieties Released in China From 1978 to 2017. FRONTIERS IN PLANT SCIENCE 2019; 10:543. [PMID: 31134107 PMCID: PMC6514245 DOI: 10.3389/fpls.2019.00543] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/09/2019] [Indexed: 05/20/2023]
Abstract
Despite evidence from previous case studies showing that agronomic traits partially determine the resulting yield of different rice (Oryza sativa L.) varieties, it remains unclear whether this is true at the ecotype level. Here, an extensive dataset of the traits of 7686 rice varieties, released in China from 1978 to 2017, was used to study the relationship between yield and other agronomic traits. We assessed the association between yield and other agronomic traits for four different rice ecotypes, i.e., indica inbred, indica hybrid, japonica inbred, and japonica hybrid. We found that associations between agronomic traits and yield were ecotype-dependent. For both the indica inbred and indica hybrid ecotypes, we found that greater values of certain traits, including the filled grain number per panicle, 1000-grain-weight, plant height, panicle length, grains per panicle, seed setting rate, long growth period, low panicle number per unit area, and low seed length/width ratio, have accounted for high grain yield. In the japonica inbred and japonica hybrid ecotypes, we found that only high panicle number per unit area and long growth period led to high grain yield. Indirectly, growth period consistently had a positive effect on yield in all ecotypes, and plant height had a positive effect on yield for the indicas and japonica inbred only. Plant height had a negative effect for the japonica hybrid. Altogether, our findings potentially have valuable implications for improving the breeds of rice ecotypes.
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Affiliation(s)
- Ronghua Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Meijuan Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Umair Ashraf
- Department of Botany, University of Education (Lahore), Faisalabad-Campus, Faisalabad, Pakistan
- College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Shiwei Liu
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
| | - Jiaen Zhang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
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Fei C, Geng X, Xu Z, Xu Q. Multiple areas investigation reveals the genes related to vascular bundles in rice. RICE (NEW YORK, N.Y.) 2019; 12:17. [PMID: 30900100 PMCID: PMC6428884 DOI: 10.1186/s12284-019-0278-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/14/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND The vascular bundle in the panicle neck is a crucial trait in rice (Oryza sativa) production that differs between the indica and japonica subspecies. However, the effect of indica/japonica genetic background on the vascular bundles remains unknown. RESULTS A series of recombinant inbred lines (RILs) derived from a cross between japonica and indica were planted in three areas. High-throughput sequencing was conducted to determine the indica pedigree percentage and for quantitative trait locus (QTL) analysis. The indica pedigree affected the number of large vascular bundles (LVBs), but not the number of small vascular bundles (SVBs). QTL analysis identified a locus (qLVB9) that was pleiotropic for both LVBs and SVBs in all three areas, and qLVB9 appeared synonymous with DENSE AND ERECT PANICLE 1 (DEP1). Using CRISPR/Cas9 gene editing and gene overexpression technology, we confirmed that the truncated dep1 allele increased the number of LVBs, and resulted in LVBs more closely associated to the indica pedigree. RNA sequencing showed that the truncated dep1 allele downregulated the AP2-like gene family. The double mutant for the DEP1 and AP2-like genes (OsAP2-39) showed decreased endogenous abscisic acid (ABA) level and insensitivity to exogenous ABA treatment, confirming that both DEP1 and OsAP2-39 are involved in the ABA response mechanism. CONCLUSIONS The present study showed the qLVB9/DEP1 affects LVBs, and involved in ABA signaling via regulating the AP2-like gene family. These results offer new insights into the function of qLVB9/DEP1 in rice.
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Affiliation(s)
- Cheng Fei
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Geng
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhengjin Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang, 110866, China.
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