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Qi G, Si Z, Xuan L, Han Z, Hu Y, Fang L, Dai F, Zhang T. Unravelling the genetic basis and regulation networks related to fibre quality improvement using chromosome segment substitution lines in cotton. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39046162 DOI: 10.1111/pbi.14436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/02/2024] [Accepted: 07/06/2024] [Indexed: 07/25/2024]
Abstract
The elucidation of genetic architecture and molecular regulatory networks underlying complex traits remains a significant challenge in life science, largely due to the substantial background effects that arise from epistasis and gene-environment interactions. The chromosome segment substitution line (CSSL) is an ideal material for genetic and molecular dissection of complex traits due to its near-isogenic properties; yet a comprehensive analysis, from the basic identification of substitution segments to advanced regulatory network, is still insufficient. Here, we developed two cotton CSSL populations on the Gossypium hirsutum background, representing wide adaptation and high lint yield, with introgression from G. barbadense, representing superior fibre quality. We sequenced 99 CSSLs that demonstrated significant differences from G. hirsutum in fibre, and characterized 836 dynamic fibre transcriptomes in three crucial developmental stages. We developed a workflow for precise resolution of chromosomal substitution segments; the genome sequencing revealed substitutions collectively representing 87.25% of the G. barbadense genome. Together, the genomic and transcriptomic survey identified 18 novel fibre-quality-related quantitative trait loci with high genetic contributions and the comprehensive landscape of fibre development regulation. Furthermore, analysis determined unique cis-expression patterns in CSSLs to be the driving force for fibre quality alteration; building upon this, the co-expression regulatory network revealed biological relationships among the noted pathways and accurately described the molecular interactions of GhHOX3, GhRDL1 and GhEXPA1 during fibre elongation, along with reliable predictions for their interactions with GhTBA8A5. Our study will enhance more strategic employment of CSSL in crop molecular biology and breeding programmes.
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Affiliation(s)
- Guoan Qi
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhanfeng Si
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lisha Xuan
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zegang Han
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Hu
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lei Fang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fan Dai
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tianzhen Zhang
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, Hainan, China
- The Advanced Seed Institute, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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Han B, Zhang W, Wang F, Yue P, Liu Z, Yue D, Zhang B, Ma Y, Lin Z, Yu Y, Wang Y, Zhang X, Yang X. Dissecting the Superior Drivers for the Simultaneous Improvement of Fiber Quality and Yield Under Drought Stress Via Genome-Wide Artificial Introgressions of Gossypium barbadense into Gossypium hirsutum. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400445. [PMID: 38984458 DOI: 10.1002/advs.202400445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/07/2024] [Indexed: 07/11/2024]
Abstract
Global water scarcity and extreme weather intensify drought stress, significantly reducing cotton yield and quality worldwide. Drought treatments are conducted using a population of chromosome segment substitution lines generated from E22 (G. hirsutum) and 3-79 (G. barbadense) as parental lines either show superior yields or fiber quality under both control and drought conditions. Fourteen datasets, covering 4 yields and 4 quality traits, are compiled and assessed for drought resistance using the drought resistance coefficient (DRC) and membership function value of drought resistance (MFVD). Genome-wide association studies, linkage analysis, and bulked segregant analysis are combined to analyze the DR-related QTL. A total of 121 significant QTL are identified by DRC and MFVD of the 8 traits. CRISPR/Cas9 and virus-induced gene silencing techniques verified DRR1 and DRT1 as pivotal genes in regulating drought resistant of cotton, with hap3-79 exhibiting greater drought resistance than hapE22 concerning DRR1 and DRT1. Moreover, 14 markers with superior yield and fiber quality are selected for drought treatment. This study offers valuable insights into yield and fiber quality variations between G. hirsutum and G. barbadense amid drought, providing crucial theoretical and technological backing for developing cotton varieties resilient to drought, with high yield and superior fiber quality.
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Affiliation(s)
- Bei Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenhao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fengjiao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pengkai Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhilin Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yu Yu
- Cotton Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, 832000, China
| | - Yanqin Wang
- College of Life Sciences, Tarim University, Alar, 843300, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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Surapaneni M, Balakrishnan D, Addanki K, Yadavalli VR, Kumar AP, Prashanthi P, Sundaram RM, Neelamraju S. Fine mapping of interspecific secondary CSSL populations revealed key regulators for grain weight at qTGW3.1 locus from Oryza nivara. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1145-1160. [PMID: 39100880 PMCID: PMC11291809 DOI: 10.1007/s12298-024-01483-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 06/14/2024] [Accepted: 06/28/2024] [Indexed: 08/06/2024]
Abstract
Grain weight (GW) is the most important stable trait that directly contributes to crop yield in case of cereals. A total of 105 backcross introgression lines (BC2F10 BILs) derived from Swarna/O. nivara IRGC81848 (NPS) and 90 BILs from Swarna/O. nivara IRGC81832 (NPK) were evaluated for thousand-grain weight (TGW) across four years (wet seasons 2014, 2015, 2016 and 2018) and chromosome segment substitution lines (CSSLs) were selected. From significant pair- wise mean comparison with Swarna, a total of 77 positively and 29 negatively significant NPS lines and 62 positively and 29 negatively significant NPK lines were identified. In all 4 years, 14 NPS lines and 9 NPK lines were positively significant and one-line NPS69 (IET22161) was negatively significant for TGW over Swarna consistently. NPS lines and NPK lines were genotyped using 111 and 140 polymorphic SSRs respectively. Quantitative trait locus (QTL) mapping using ICIM v4.2 software showed 13 QTLs for TGW in NPS. Three major effect QTLs qTGW2.1, qTGW8.1 and qTGW11.1 were identified in NPS for two or more years with PVE ranging from 8 to 14%. Likewise, 10 QTLs were identified in NPK and including two major effect QTL qTGW3.1 and qTGW12.1 with 6 to 32% PVE. In all QTLs, O. nivara alleles increased TGW. These consistent QTLs are very suitable for fine mapping and functional analysis of grain weight. Further in this study, CSSLs NPS1 (10-2S) and NPK61 (158 K) with significantly higher grain weight than the recurrent parent, Swarna cv. Oryza sativa were selected from each population and secondary F2 mapping populations were developed. Using Bulked Segregant QTL sequencing, a grain weight QTL, designated as qTGW3.1 was fine mapped from the cross between NPK61 and Swarna. This QTL explained 48% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 31 kb interval using recombinant analysis. GRAS transcription factor gene (OS03go103400) involved in plant growth and development located at this genomic locus might be the candidate gene for qTGW3.1. The results of this study will help in further functional studies and improving the knowledge related to the molecular mechanism of grain weight in Oryza and lays a solid foundation for the breeding for high yield. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01483-0.
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Affiliation(s)
- Malathi Surapaneni
- ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, Telangana 500 030 India
| | - Divya Balakrishnan
- ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, Telangana 500 030 India
| | - Krishnamraju Addanki
- ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, Telangana 500 030 India
| | | | - Arun Prem Kumar
- ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, Telangana 500 030 India
| | - P. Prashanthi
- ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, Telangana 500 030 India
| | - R. M. Sundaram
- ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, Telangana 500 030 India
| | - Sarla Neelamraju
- ICAR-Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad, Telangana 500 030 India
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Huang J, Zhang Y, Li Y, Xing M, Lei C, Wang S, Nie Y, Wang Y, Zhao M, Han Z, Sun X, Zhou H, Wang Y, Zheng X, Xiao X, Fan W, Liu Z, Guo W, Zhang L, Cheng Y, Qian Q, He H, Yang Q, Qiao W. Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice. Nat Commun 2024; 15:4573. [PMID: 38811581 PMCID: PMC11137157 DOI: 10.1038/s41467-024-48845-6] [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: 02/14/2023] [Accepted: 05/15/2024] [Indexed: 05/31/2024] Open
Abstract
The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.
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Affiliation(s)
- Jingfen Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yilin Zhang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Yapeng Li
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
- Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Meng Xing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Cailin Lei
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Shizhuang Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Yamin Nie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Yanyan Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Mingchao Zhao
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
- Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Zhenyun Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianjun Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Zhou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Yan Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Xiaoming Zheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Xiaorong Xiao
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
- Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Weiya Fan
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziran Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenlong Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunlian Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Qian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China.
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
| | - Qingwen Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China.
| | - Weihua Qiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China.
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5
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Jong C, Yu Z, Zhang Y, Choe K, Uh S, Kim K, Jong C, Cha J, Kim M, Kim Y, Han X, Yang M, Xu C, Hu L, Chen Q, Liu C, Qi Z. Multi-Omics Analysis of a Chromosome Segment Substitution Line Reveals a New Regulation Network for Soybean Seed Storage Profile. Int J Mol Sci 2024; 25:5614. [PMID: 38891802 PMCID: PMC11171932 DOI: 10.3390/ijms25115614] [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: 04/06/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 06/21/2024] Open
Abstract
Soybean, a major source of oil and protein, has seen an annual increase in consumption when used in soybean-derived products and the broadening of its cultivation range. The demand for soybean necessitates a better understanding of the regulatory networks driving storage protein accumulation and oil biosynthesis to broaden its positive impact on human health. In this study, we selected a chromosome segment substitution line (CSSL) with high protein and low oil contents to investigate the underlying effect of donor introgression on seed storage through multi-omics analysis. In total, 1479 differentially expressed genes (DEGs), 82 differentially expressed proteins (DEPs), and 34 differentially expressed metabolites (DEMs) were identified in the CSSL compared to the recurrent parent. Based on Gene Ontology (GO) term analysis and the Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG), integrated analysis indicated that 31 DEGs, 24 DEPs, and 13 DEMs were related to seed storage functionality. Integrated analysis further showed a significant decrease in the contents of the seed storage lipids LysoPG 16:0 and LysoPC 18:4 as well as an increase in the contents of organic acids such as L-malic acid. Taken together, these results offer new insights into the molecular mechanisms of seed storage and provide guidance for the molecular breeding of new favorable soybean varieties.
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Affiliation(s)
- Cholnam Jong
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Zhenhai Yu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
- Heilongjiang Green Food Science Research Institute, Harbin 150000, China
| | - Yu Zhang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Kyongho Choe
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Songrok Uh
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Kibong Kim
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Chol Jong
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Jinmyong Cha
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Myongguk Kim
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Yunchol Kim
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Xue Han
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Mingliang Yang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Chang Xu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Limin Hu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Qingshan Chen
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Chunyan Liu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
| | - Zhaoming Qi
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (C.J.); (Z.Y.); (Y.Z.); (K.C.); (S.U.); (K.K.); (C.J.); (J.C.); (M.K.); (Y.K.); (X.H.); (M.Y.); (C.X.); (L.H.); (C.L.)
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6
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Kapoor C, Anamika, Mukesh Sankar S, Singh SP, Singh N, Kumar S. Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet. PLANTA 2024; 259:155. [PMID: 38750378 DOI: 10.1007/s00425-024-04423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
MAIN CONCLUSION Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.
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Affiliation(s)
- Chandan Kapoor
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Anamika
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Mukesh Sankar
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - S P Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nirupma Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sudhir Kumar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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7
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Xing M, Nie Y, Huang J, Li Y, Zhao M, Wang S, Wang Y, Chen W, Chen Z, Zhang L, Cheng Y, Yang Q, Sun J, Qiao W. A wild rice CSSL population facilitated identification of salt tolerance genes and rice germplasm innovation. PHYSIOLOGIA PLANTARUM 2024; 176:e14301. [PMID: 38629128 DOI: 10.1111/ppl.14301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/31/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Salt stress is one of the major factors that limits rice production. Therefore, identification of salt-tolerant alleles from wild rice is important for rice breeding. In this study, we constructed a set of chromosome segment substitution lines (CSSLs) using wild rice as the donor parent and cultivated rice Nipponbare (Nip) as the recurrent parent. Salt tolerance germinability (STG) was evaluated, and its association with genotypes was determined using this CSSL population. We identified 17 QTLs related to STG. By integrating the transcriptome and genome data, four candidate genes were identified, including the previously reported AGO2 and WRKY53. Compared with Nip, wild rice AGO2 has a structure variation in its promoter region and the expression levels were upregulated under salt treatments; wild rice WRKY53 also has natural variation in its promoter region, and the expression levels were downregulated under salt treatments. Wild rice AGO2 and WRKY53 alleles have combined effects for improving salt tolerance at the germination stage. One CSSL line, CSSL118 that harbors these two alleles was selected. Compared with the background parent Nip, CSSL118 showed comprehensive salt tolerance and higher yield, with improved transcript levels of reactive oxygen species scavenging genes. Our results provided promising genes and germplasm resources for future rice salt tolerance breeding.
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Affiliation(s)
- Meng Xing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Yamin Nie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Jingfen Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Yapeng Li
- Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Mingchao Zhao
- Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Shizhuang Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Yanyan Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Wenxi Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziyi Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Lifang Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunlian Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingwen Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, China
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8
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Li H, Zhu L, Fan R, Li Z, Liu Y, Shaheen A, Nie F, Li C, Liu X, Li Y, Liu W, Yang Y, Guo T, Zhu Y, Bu M, Li C, Liang H, Bai S, Ma F, Guo G, Zhang Z, Huang J, Zhou Y, Song CP. A platform for whole-genome speed introgression from Aegilops tauschii to wheat for breeding future crops. Nat Protoc 2024; 19:281-312. [PMID: 38017137 DOI: 10.1038/s41596-023-00922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/28/2023] [Indexed: 11/30/2023]
Abstract
Breeding new and sustainable crop cultivars of high yields and desirable traits has been a major challenge for ensuring food security for the growing global human population. For polyploid crops such as wheat, introducing genetic variation from wild relatives of its subgenomes is a key strategy to improve the quality of their breeding pools. Over the past decades, considerable progress has been made in speed breeding, genome sequencing, high-throughput phenotyping and genomics-assisted breeding, which now allows us to realize whole-genome introgression from wild relatives to modern crops. Here, we present a standardized protocol to rapidly introgress the entire genome of Aegilops tauschii, the progenitor of the D subgenome of bread wheat, into elite wheat backgrounds. This protocol integrates multiple modern high-throughput technologies and includes three major phases: development of synthetic octaploid wheat, generation of hexaploid A. tauschii-wheat introgression lines (A-WIs) and homozygosis of the generated A-WIs. Our approach readily generates stable introgression lines in 2 y, thus greatly accelerating the generation of A-WIs and the introduction of desirable genes from A. tauschii to wheat cultivars. These A-WIs are valuable for wheat-breeding programs and functional gene discovery. The current protocol can be easily modified and used for introgressing the genomes of wild relatives to other polyploid crops.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, China
| | - Lele Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Ruixiao Fan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Zheng Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yifan Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Aaqib Shaheen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Fang Nie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Can Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Xuqin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yuanyuan Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Wenjuan Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yingying Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Tutu Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yu Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Mengchen Bu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Chenglin Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Huihui Liang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Feifei Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Guanghui Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, China
| | - Zhen Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng, China
| | - Jinling Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China.
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China.
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Deng K, Zhang H, Wu J, Zhao Z, Wang D, Xu G, Yu J, Ling Y, Zhao F. Development of Single-Segment Substitution Lines and Fine-Mapping of qSPP4 for Spikelets Per Panicle and qGW9 for Grain Width Based on Rice Dual-Segment Substitution Line Z783. Int J Mol Sci 2023; 24:17305. [PMID: 38139135 PMCID: PMC10744095 DOI: 10.3390/ijms242417305] [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: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Single segment substitution line (SSSL) libraries are an ideal platform for breeding by design. To develop SSSLs-Xihui18 covering the whole genome, a novel rice chromosome segment substitution line (CSSL), Z783, carrying two substitution segments (average length of 6.55 Mb) on Chr.4 and Chr.9 was identified, which was a gap in the library previously. Z783 was developed from the progeny of recipient "Xihui18" (an indica restorer line) and donor "Huhan3" (a japonica cultivar) by advanced backcross combined molecular marker-assisted selection (MAS). It displayed multiple panicles and less spikelets and wide grains. Then, a F2 population derived from Xihui18/Z783 was used to map quantitative trait loci (QTLs) for yield-related traits by the mixed linear model method. Nine QTLs were detected (p < 0.05). Furthermore, three SSSLs were constructed by MAS, and all 9 QTLs could be validated, and 15 novel QTLs could be detected by these SSSLs by a one-way ANOVA analysis. The genetic analysis showed that qSSP4 for less spikelets and qGW9 for wide grain all displayed dominant gene action in their SSSLs. Finally, qSSP4 and qGW9 were fine-mapped to intervals of 2.75 Mb and 1.84 Mb, on Chromosomes 4 and 9, respectively. The results lay a solid foundation for their map cloning and molecular breeding by design.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Science, Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China; (K.D.); (H.Z.); (J.W.); (Z.Z.); (D.W.); (G.X.); (J.Y.); (Y.L.)
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10
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Adam H, Gutiérrez A, Couderc M, Sabot F, Ntakirutimana F, Serret J, Orjuela J, Tregear J, Jouannic S, Lorieux M. Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture. BMC Genomics 2023; 24:587. [PMID: 37794325 PMCID: PMC10548634 DOI: 10.1186/s12864-023-09695-6] [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: 07/07/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied. RESULTS To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. CONCLUSION Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.
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Affiliation(s)
- Hélène Adam
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | | | - Marie Couderc
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - François Sabot
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | | | - Julien Serret
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Julie Orjuela
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - James Tregear
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Stefan Jouannic
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | - Mathias Lorieux
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Cali, Colombia.
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11
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Sun W, Sun Q, Tian L, Sun Y, Yu S. A Structure Variation in qPH8.2 Detrimentally Affects Plant Architecture and Yield in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3336. [PMID: 37765500 PMCID: PMC10536775 DOI: 10.3390/plants12183336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
Plant height is an important agronomic trait associated with plant architecture and grain yield in rice (Oryza sativa L.). In this study, we report the identification of quantitative trait loci (QTL) for plant height using a chromosomal segment substitution line (CSSL) population with substituted segments from japonica variety Nipponbare (NIP) in the background of the indica variety 9311. Eight stable QTLs for plant height were identified in three environments. Among them, six loci were co-localized with known genes such as semidwarf-1 (sd1) and Grain Number per Panicle1 (GNP1) involved in gibberellin biosynthesis. A minor QTL qPH8.2 on chromosome 8 was verified and fine-mapped to a 74 kb region. Sequence comparison of the genomic region revealed the presence/absence of a 42 kb insertion between NIP and 9311. This insertion occurred predominantly in temperate japonica rice. Comparisons on the near-isogenic lines showed that the qPH8.2 allele from NIP exhibits pleiotropic effects on plant growth, including reduced plant height, leaf length, photosynthetic capacity, delayed heading date, decreased yield, and increased tiller angle. These results indicate that qPH8.2 from temperate japonica triggers adverse effects on plant growth and yield when introduced into the indica rice, highlighting the importance of the inter-subspecies crossing breeding programs.
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Affiliation(s)
- Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.S.); (Y.S.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.S.); (L.T.)
| | - Li Tian
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.S.); (L.T.)
| | - Yongjian Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.S.); (Y.S.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.S.); (L.T.)
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (W.S.); (Y.S.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.S.); (L.T.)
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12
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Wang Z, Guo Z, Zou T, Zhang Z, Zhang J, He P, Song R, Liu Z, Zhu H, Zhang G, Fu X. Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara. RICE (NEW YORK, N.Y.) 2023; 16:38. [PMID: 37668809 PMCID: PMC10480103 DOI: 10.1186/s12284-023-00655-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Domestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be progenitors of O. sativa. RESULTS In the present study, by using O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSLs) have been developed in the background of the elite indica cultivar, HJX74. In the SSSLs population, 11 genes for 5 domestication traits, including tiller angle, spreading panicle, awn, seed shattering, and red pericarp, were identified and mapped on 5 chromosomes through substitution mapping. Herein, allelic variations of 7 genes were found through sequence alignment with the known genes, that is, TA7-RUF was allelic to PROG1, TA8-RUF was allelic to TIG1, SPR4-NIV was allelic to OsLG1, AN4-RUF was allelic to An-1, SH4-NIV was allelic to SH4, and both RC7-RUF and RC7-NIV were allelic to Rc. Meanwhile, 4 genes, TA11-NIV, SPR3-NIV, AN3-NIV, and AN4-NIV, were considered as the novel genes identified in these SSSLs, because of none known genes for the related domestication traits found in the chromosomal locations of them. CONCLUSION The results indicated that the SSSLs would be precious germplasm resources for gene mining and utilization from wild rice species, and it laid the foundation for further analyses of the novel domestication genes to better understand the genetic basis in regulating the traits variation during domestication.
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Affiliation(s)
- Zhangqiang Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zisheng Guo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Tuo Zou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhe Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ping He
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ruifeng Song
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ziqiang Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| | - Xuelin Fu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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13
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Xu G, Deng K, Yu J, Li Q, Li L, Xiang A, Ling Y, Zhang C, Zhao F. Genetic Effects Analysis of QTLs for Rice Grain Size Based on CSSL-Z403 and Its Dissected Single and Dual-Segment Substitution Lines. Int J Mol Sci 2023; 24:12013. [PMID: 37569388 PMCID: PMC10418668 DOI: 10.3390/ijms241512013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Rice chromosomal segment substitution lines (CSSLs) are ideal materials for studying quantitative traits such as grain size. Here, a rice large-grain CSSL-Z403 was identified among progeny of the recipient Xihui18 and the donor Jinhui35 based on molecular marker-assisted selection. Z403 carried 10 substitution segments with average length of 3.01 Mb. Then, a secondary F2 population derived from a cross between Xihui18 and Z403 was used to map quantitative trait loci (QTL) for grain size. Six QTLs distributed on chromosomes 5, 6, 7, 9 and 12 were detected. Finally four single-segment substitution lines (SSSLs) and two dual-segment substitution lines (DSSLs) carrying these target QTLs were constructed, and 10 novel QTLs were identified by four SSSLs. The large grain of Z403 was controlled at least by qGWT5, qGWT7, qGWT9 and qGWT12, and its grain weight was influenced through grain length QTL such as qGL5, qGL6, qGL9 and qGL12, as well as grain width QTL such as qGW5, qGW7, qGW9 and qGW12. Among 16 QTLs, four QTLs including qGL6, etc., might be novel compared with the reported documents. Again, positive or less negative epistatic effects between two non-allelic QTLs (additive effect > 0) may assist screening the genotype with larger grain size in further selection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Science, Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China; (G.X.)
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14
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Nagata K, Nonoue Y, Matsubara K, Mizobuchi R, Ono N, Shibaya T, Ebana K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru JI, Uga Y, Fukuda A, Ueda T, Yamamoto SI, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Sun J, Kuya N, Kitomi Y, Iijima K, Nagasaki H, Shomura A, Mizubayashi T, Kitazawa N, Hori K, Ando T, Yamamoto T, Fukuoka S, Yano M. Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice. BREEDING SCIENCE 2023; 73:332-342. [PMID: 37840983 PMCID: PMC10570878 DOI: 10.1270/jsbbs.23006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 10/17/2023]
Abstract
Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the japonica background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice. Using these materials, we overviewed the chromosomal locations of 1079 putative QTLs for seven agronomic traits and their allelic distribution in Asian cultivated rice through multiple linear regression analysis. The CSSLs will allow the effects of putative QTLs in the highly homogeneous japonica background to be validated.
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Affiliation(s)
- Kazufumi Nagata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yasunori Nonoue
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuki Matsubara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ritsuko Mizobuchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Taeko Shibaya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kaworu Ebana
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eri Ogiso-Tanaka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takanari Tanabata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuhiko Sugimoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fumio Taguchi-Shiobara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jun-ichi Yonemaru
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yusaku Uga
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Atsunori Fukuda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tadamasa Ueda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shin-ichi Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Utako Yamanouchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshiyuki Takai
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takashi Ikka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Katsuhiko Kondo
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tomoki Hoshino
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eiji Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shunsuke Adachi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jian Sun
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kuya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yuka Kitomi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ken Iijima
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hideki Nagasaki
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ayahiko Shomura
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tatsumi Mizubayashi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kitazawa
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kiyosumi Hori
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tsuyu Ando
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshio Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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Yang Y, You C, Wang N, Wu M, Le Y, Wang M, Zhang X, Yu Y, Lin Z. Gossypium mustelinum genome and an introgression population enrich interspecific genetics and breeding in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:130. [PMID: 37199762 DOI: 10.1007/s00122-023-04379-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Genomic and genetic resources of G. mustelinum were effective for identifying genes for qualitative and quantitative traits. Gossypium mustelinum represents the earliest diverging evolutionary lineage of polyploid Gossypium, representing a rich gene pool for numerous desirable traits lost in cotton cultivars. Accurate information of the genomic features and the genetic architecture of objective traits are essential for the discovery and utilization of G. mustelinum genes. Here, we presented a chromosome-level genome assembly of G. mustelinum and developed an introgression population of the G. mustelinum in the background of G. hirsutum that contained 264 lines. We precisely delimited the boundaries of the 1,662 introgression segments with the help of G. mustelinum genome assembly, and 87% of crossover regions (COs) were less than 5 Kb. Genes for fuzzless and green fuzz were discovered, and a total of 14 stable QTLs were identified with 12 novel QTLs across four independent environments. A new fiber length QTL, qUHML/SFC-A11, was confined to a 177-Kb region, and GmOPB4 and GmGUAT11 were considered as the putative candidate genes as potential negative regulator for fiber length. We presented a genomic and genetic resource of G. mustelinum, which we demonstrated that it was efficient for identifying genes for qualitative and quantitative traits. Our study built a valuable foundation for cotton genetics and breeding.
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Affiliation(s)
- Yang Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Institute of Nuclear and Biotechnology, Xinjiang Academy of Agricultural Sciences/Xinjiang Key Laboratory of Crop Biotechnology/The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Urumqi, 830091, Xinjiang, China
| | - Chunyuan You
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, 832000, Xinjiang, China
| | - Nian Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mi Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yu Le
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yu Yu
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, 832000, Xinjiang, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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16
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Vasisth P, Singh N, Limbalkar OM, Sharma M, Dhanasekaran G, Meena ML, Jain P, Jaiswal S, Iquebal MA, Watts A, Gaikwad KB, Singh R. Introgression of Heterotic Genomic Segments from Brassica carinata into Brassica juncea for Enhancing Productivity. PLANTS (BASEL, SWITZERLAND) 2023; 12:1677. [PMID: 37111905 PMCID: PMC10146992 DOI: 10.3390/plants12081677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/18/2023] [Accepted: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Interspecific hybridization resulted in the creation of B. juncea introgression lines (ILs) generated from B. carinata with increased productivity and adaptability. Forty ILs were crossed with their respective B. juncea recipient parents to generate introgression line hybrids (ILHs) and the common tester (SEJ 8) was used to generate test hybrids (THs). Mid-parent heterosis in ILHs and standard heterosis in THs were calculated for eight yield and yield-related traits. Heterotic genomic regions were dissected using ten ILs with significant mid-parent heterosis in ILHs and standard heterosis in THs for seed yield. A high level of heterosis for seed yield was contributed by 1000 seed weight (13.48%) in D31_ILHs and by total siliquae/plant (14.01%) and siliqua length (10.56%) in PM30_ILHs. The heterotic ILs of DRMRIJ 31 and Pusa Mustard 30 were examined using polymorphic SNPs between the parents, and a total of 254 and 335 introgressed heterotic segments were identified, respectively. This investigation discovered potential genes, viz., PUB10, glutathione S transferase, TT4, SGT, FLA3, AP2/ERF, SANT4, MYB, and UDP-glucosyl transferase 73B3 that were previously reported to regulate yield-related traits. The heterozygosity of the FLA3 gene significantly improved siliqua length and seeds per siliqua in ILHs of Pusa Mustard 30. This research proved that interspecific hybridization is an effective means of increasing the diversity of cultivated species by introducing new genetic variants and improving the level of heterosis.
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Affiliation(s)
- Prashant Vasisth
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Naveen Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Omkar Maharudra Limbalkar
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Mohit Sharma
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Gokulan Dhanasekaran
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Mohan Lal Meena
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priyanka Jain
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Anshul Watts
- Indian Council of Agricultural Research-National Institute of Plant Biotechnology, New Delhi 110012, India
| | - Kiran B. Gaikwad
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rajendra Singh
- Division of Genetics, Indian Council of Agricultural Research-Indian Agricultural Research Institute, New Delhi 110012, India
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Tomita R, Reyes VP, Fukuta Y, Gichuhi EW, Kikuta M, Menge DM, Doi K, Makihara D. Genetic Variation of Blast ( Pyricularia oryzae Cavara) Resistance in the Longistaminata Chromosome Segment Introgression Lines (LCSILs) and Potential for Breeding Use in Kenya. PLANTS (BASEL, SWITZERLAND) 2023; 12:863. [PMID: 36840212 PMCID: PMC9966461 DOI: 10.3390/plants12040863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In Kenya's rice-growing areas, Basmati varieties have been produced in monoculture since the late 1980s. This has resulted in the breakdown of the resistance (R) gene-mediated response of the local Basmati varieties to blast disease caused by Pyricularia oryzae. To improve blast resistance in Kenyan Basmati varieties, continuous identification of R genes and suitable breeding materials for Basmati are necessary. Longistaminata chromosome segment introgression lines (LCSILs) with the Kernel Basmati genetic background, developed using a rice line called potential low-input adaptable-1 (pLIA-1) derived from a cross between Taichung 65 (T65) (a rice variety in the Japonica Group) and O. longistaminata, are expected to contain useful blast R genes derived from O. longistaminata or T65. In this study, we investigated the genetic variation of blast R genes in LCSILs and their parents by using a new international differential system for designating blast races based on the gene-for-gene theory and molecular characterization using single nucleotide polymorphism (SNP) markers. LCSILs and their parents were classified into three groups-A, B1, and B2-based on reaction patterns to the standard differential blast isolates (SDBIs). Group A, including pLIA-1, showed the highest resistance in all groups, followed by groups B1 and B2. Kernel Basmati in group B1 was considered to possess Pik-p or Pi7(t), Pi19(t), and other unknown R genes. In addition to these R genes, LCSIL 6, 12, 27, 28, and 40, in group A, were determined to possess one of Pish, Piz-t, or both genes that confer resistance to the Kenyan blast races. These lines can be used for efficiently pyramiding blast R genes in the local Basmati varieties.
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Affiliation(s)
- Rena Tomita
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Vincent Pamugas Reyes
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshimichi Fukuta
- Japan International Research Center for Agricultural Sciences, Tsukuba 305-8686, Japan
| | - Emily Waringa Gichuhi
- Kenya Agricultural and Livestock Research Organization, Kerugoya P.O. Box 298-10300, Kenya
| | - Mayumi Kikuta
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Daniel Makori Menge
- Kenya Agricultural and Livestock Research Organization, Kerugoya P.O. Box 298-10300, Kenya
| | - Kazuyuki Doi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Daigo Makihara
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya 464-8601, Japan
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Zhang Y, Qin Y, Li D, Wang W, Gao X, Hao C, Feng H, Wang Y, Li T. Fine mapping and cloning of a novel BrSCC1 gene for seed coat color in Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:11. [PMID: 36658295 DOI: 10.1007/s00122-023-04287-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
A novel BrSCC1 gene for seed coat color was fine mapped within a 41.1-kb interval on chromosome A03 in Brassica rapa and functionally validated by ectopic expression analysis. Yellow seed is a valuable breeding trait that can be potentiality applied for improving seed quality and oil productivity in oilseed Brassica crops. However, only few genes for yellow seed have been identified in B. rapa. We previously identified a minor quantitative trait locus (QTL), qSC3.1, for seed coat color on chromosome A03 in B. rapa. In order to isolate the seed coat color gene, a brown-seeded chromosome segment substitution line, CSSL-38, harboring the qSC3.1, was selected and crossed with the yellow-seeded recurrent parent, a rapid cycling inbred line of B. rapa (RcBr), to construct the secondary F2 population. Metabolite identification suggested that seed coat coloration in CSSL-38 was independent of proanthocyanidins (PAs) accumulation. Genetic analysis revealed that yellow seed was controlled by a single recessive gene, Seed Coat Color 1 (BrSCC1). Utilizing bulked segregant analysis (BSA)-seq and secondary F2 and F2:3 recombinants analysis, BrSCC1 was fine mapped within a 41.1-kb interval. By integrating gene expression profiling, genome sequence comparison, metabolite analysis, and functional validation through ectopic expression in Arabidopsis, the BraA03g040800.3C gene was confirmed to be BrSCC1, which positively correlated with the seed coat coloration. Our study provides a novel gene resource for the genetic improvement of yellow seeds in oilseed B. rapa.
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Affiliation(s)
- Yinghuan Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yao Qin
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Dongxiao Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xu Gao
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Chunming Hao
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yugang Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, People's Republic of China.
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, People's Republic of China
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19
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Li S, Zou J, Fan J, Guo D, Tan L. Identification of quantitative trait loci for important agronomic traits using chromosome segment substitution lines from a japonica × indica cross in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:73. [PMID: 37313327 PMCID: PMC10248660 DOI: 10.1007/s11032-022-01343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/15/2022] [Indexed: 06/15/2023]
Abstract
Asian cultivated rice (Oryza sativa L.) has two subspecies, indica and japonica, which display clear differences in yield-related traits and environmental adaptation. Here, we developed a set of chromosome segment substitution lines (CSSLs) from an advanced backcross between japonica variety C418, as the recipient, and indica variety IR24, as the donor. Through evaluating the genotypes and phenotypes of 181 CSSLs, a total of 85 quantitative trait loci (QTLs) for 14 yield-related traits were detected, with individual QTLs explaining from 6.2 to 42.9% of the phenotypic variation. Moreover, twenty-six of these QTLs could be detected in the two trial sites (Beijing and Hainan). Among these loci, the QTLs for flag leaf width and effective tiller number, qFLW4.2 and qETN4.2, were delimited to an approximately 256-kb interval on chromosome 4. Through a comparison of nucleotide sequences and expression levels in "C418" and the CSSL CR31 containing qFLW4.2 and qETN4.2, we found that the NAL1 (LOC_Os04g52479) gene was the candidate gene for qFLW4.2 and qETN4.2. Our results show that CSSLs are powerful tools for identifying and fine-mapping QTLs, while the novel QTLs identified in this study will also provide new genetic resources for rice improvement. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01343-3.
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Affiliation(s)
- Shuangzhe Li
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Jun Zou
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Jinjian Fan
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Daokuan Guo
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
| | - Lubin Tan
- State Key Laboratory of Agrobiotechnology, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193 China
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20
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Santo Domingo M, Mayobre C, Pereira L, Argyris J, Valverde L, Martín-Hernández AM, Garcia-Mas J, Pujol M. Fruit Morphology and Ripening-Related QTLs in a Newly Developed Introgression Line Collection of the Elite Varieties 'Védrantais' and 'Piel de Sapo'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223120. [PMID: 36432848 PMCID: PMC9694011 DOI: 10.3390/plants11223120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 11/10/2022] [Indexed: 05/28/2023]
Abstract
Melon is an economically important crop with widely diverse fruit morphology and ripening characteristics. Its diploid sequenced genome and multiple genomic tools make this species suitable to study the genetic architecture of fruit traits. With the development of this introgression line population of the elite varieties 'Piel de Sapo' and 'Védrantais', we present a powerful tool to study fruit morphology and ripening traits that can also facilitate characterization or pyramidation of QTLs in inodorous melon types. The population consists of 36 lines covering almost 98% of the melon genome, with an average of three introgressions per chromosome and segregating for multiple fruit traits: morphology, ripening and quality. High variability in fruit morphology was found within the population, with 24 QTLs affecting six different traits, confirming previously reported QTLs and two newly detected QTLs, FLQW5.1 and FWQW7.1. We detected 20 QTLs affecting fruit ripening traits, six of them reported for the first time, two affecting the timing of yellowing of the rind (EYELLQW1.1 and EYELLQW8.1) and four at the end of chromosome 8 affecting aroma, abscission and harvest date (EAROQW8.3, EALFQW8.3, ABSQW8.3 and HARQW8.3). We also confirmed the location of several QTLs, such as fruit-quality-related QTLs affecting rind and flesh appearance and flesh firmness.
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Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Lara Pereira
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Jason Argyris
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), 08193 Barcelona, Spain
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21
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Yadavalli VR, Balakrishnan D, Surapaneni M, Addanki K, Mesapogu S, Beerelli K, Desiraju S, Voleti SR, Neelamraju S. Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon. PLANTA 2022; 256:71. [PMID: 36070104 DOI: 10.1007/s00425-022-03983-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Identification of trait enhancing QTLs for yield and photosynthesis-related traits in rice using interspecific mapping population and chromosome segment substitution lines derived from a cross between Oryza sativa and Oryza rufipogon. Wild rice contains novel genes which can help in improving rice yield. Common wild rice Oryza rufipogon is a known source for enhanced photosynthesis and yield-related traits. We developed BC2F2:3:4 mapping populations using O. rufipogon IC309814 with high photosynthetic rate as donor, and elite cultivar MTU1010 as recurrent parent. Evaluation of 238 BC2F2 families for 13 yield-related traits and 208 BC2F2 families for seven photosynthesis-related physiological traits resulted in identification of significantly different lines which performed better than MTU1010 for various yield contributing traits. 49 QTLs were identified for 13 yield traits and 7 QTLs for photosynthesis-related traits in BC2F2. In addition, 34 QTLs in BC2F3 and 26 QTLs in BC2F4 were also detected for yield traits.11 common QTLs were identified in three consecutive generations and their trait-increasing alleles were derived from O. rufipogon. Significantly, one major effect common QTL qTGW3.1 for thousand grain weight with average phenotypic variance 8.1% and one novel QTL qBM7.1 for biomass were identified. Photosynthesis-related QTLs qPN9.1, qPN12.1, qPN12.2 qSPAD1.1 and qSPAD6.1 showed additive effect from O. rufipogon. A set of 145 CSSLs were identified in BC2F2 which together represented 87% of O. rufipogon genome. In addition, 87 of the 145 CSSLs were significantly different than MTU1010 for at least one trait. The major effect QTLs can be fine mapped for gene discovery. CSSLs developed in this study are a good source of novel alleles from O. rufipogon in the background of Cottondora Sannalu for rapid improvement of any trait in rice.
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Affiliation(s)
- Venkateswara Rao Yadavalli
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Divya Balakrishnan
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
- Department of Plant Breeding and Genetics, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Malathi Surapaneni
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Krishnamraju Addanki
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sukumar Mesapogu
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Kavitha Beerelli
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Subrahmanyam Desiraju
- Department of Plant Physiology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sitapati Rao Voleti
- Department of Plant Physiology, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India
| | - Sarla Neelamraju
- ICAR National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, Telangana, India.
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22
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Mapping and Validation of qHD7b: Major Heading-Date QTL Functions Mainly under Long-Day Conditions. PLANTS 2022; 11:plants11172288. [PMID: 36079670 PMCID: PMC9459803 DOI: 10.3390/plants11172288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/16/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022]
Abstract
Heading date (HD) is one of the agronomic traits that influence maturity, regional adaptability, and grain yield. The present study was a follow-up of a previous quantitative trait loci (QTL) mapping study conducted on three populations, which uncovered a total of 62 QTLs associated with 10 agronomic traits. Two of the QTLs for HD on chromosome 7 (qHD7a and qHD7b) had a common flanking marker (RM3670) that may be due to tight linkage, and/or weakness of the statistical method. The objectives of the present study were to map QTLs associated with HD in a set of 76 chromosome segment substitution lines (CSSLs), fine map and validate one of the QTLs (qHD7b) using 2997 BC5F2:3 plants, and identify candidate genes using sequencing and expression analysis. Using the CSSLs genotyped with 120 markers and evaluated under two short-day and two long-day growing conditions, we uncovered a total of fourteen QTLs (qHD2a, qHD4a, qHD4b, qHD5a, qHD6a, qHD6b, qHD7b, qHD7c, qHD8a, qHD10a, qHD10b, qHD11a, qHD12a, and qHD12b). However, only qHD6a and qHD7b were consistently detected in all four environments. The phenotypic variance explained by qHD6a and qHD7b varied from 10.1% to 36.1% (mean 23.1%) and from 8.1% to 32.8% (mean 20.5%), respectively. One of the CSSL lines (CSSL52), which harbored a segment from the early heading XieqingzaoB (XQZB) parent at the qHD7b locus, was then used to develop a BC5F2:3 population for fine mapping and validation. Using a backcross population evaluated for four seasons under different day lengths and temperatures, the qHD7b interval was delimited to a 912.7-kb region, which is located between RM5436 and RM5499. Sequencing and expression analysis revealed a total of 29 candidate genes, of which Ghd7 (Os07g0261200) is a well-known gene that affects heading date, plant height, and grain yield in rice. The ghd7 mutants generated through CRISPR/Cas9 gene editing exhibited early heading. Taken together, the results from both the previous and present study revealed a consistent QTL for heading date on chromosome 7, which coincided not only with the physical position of a known gene, but also with two major effect QTLs that controlled the stigma exertion rate and the number of spikelets in rice. The results provide contributions to the broader adaptability of marker-assisted breeding to develop high-yield rice varieties.
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23
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Qu G, Gao Y, Wang X, Fu W, Sun Y, Gao X, Wang W, Hao C, Feng H, Wang Y. Fine mapping and analysis of candidate genes for qFT7.1, a major quantitative trait locus controlling flowering time in Brassica rapa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2233-2246. [PMID: 35532733 DOI: 10.1007/s00122-022-04108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
qFT7.1, a major QTL for flowering time in Brassica rapa was fine-mapped to chromosome A07 in a 56.4-kb interval, in which the most likely candidate gene is BraA07g018240.3C. In Brassica rapa, flowering time (FT) is an important agronomic trait that affects the yield, quality, and adaption. FT is a complicated trait that is regulated by many genes and is affected greatly by the environment. In this study, a chromosome segment substitution line (CSSL), CSSL16, was selected that showed later flowering than the recurrent parent, a rapid-cycling inbred line of B. rapa (RcBr). Using Bulked Segregant RNA sequencing, we identified a late flowering quantitative trait locus (QTL), designated as qFT7.1, on chromosome A07, based on a secondary-F2 population derived from the cross between CSSL16 and RcBr. qFT7.1 was further validated by conventional QTL mapping. This QTL explained 39.9% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 56.4-kb interval using recombinant analysis. Expression analysis suggested that BraA07g018240.3C, which is homologous to ATC (encoding Arabidopsis thaliana CENTRORADIALIS homologue), a gene for delayed flowering in Arabidopsis, as the most promising candidate gene. Sequence analysis demonstrated that two synonymous mutations existed in the coding region and numerous bases replacements existed in promoter region between BraA07g018240.3C from CSSL16 and RcBr. The results will increase our knowledge related to the molecular mechanism of late flowering in B. rapa and lays a solid foundation for the breeding of late bolting B. rapa.
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Affiliation(s)
- Gaoyang Qu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yue Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xian Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Fu
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yunxia Sun
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Xu Gao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Wei Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Chunming Hao
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Yugang Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, People's Republic of China.
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
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24
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Zheng H, Hou L, Xie J, Cao F, Wei R, Yang M, Qi Z, Zhu R, Zhang Z, Xin D, Li C, Liu C, Jiang H, Chen Q. Construction of Chromosome Segment Substitution Lines and Inheritance of Seed-Pod Characteristics in Wild Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:869455. [PMID: 35783974 PMCID: PMC9247457 DOI: 10.3389/fpls.2022.869455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Genetic populations provide the basis for genetic and genomic research, and chromosome segment substitution lines (CSSLs) are a powerful tool for the fine mapping of quantitative traits, new gene mining, and marker-assisted breeding. In this study, 213 CSSLs were obtained by self-crossing, backcrossing, and marker-assisted selection between cultivated soybean (Glycine max [L.] Merr.) variety Suinong14 (SN14) and wild soybean (Glycine soja Sieb. et Zucc.) ZYD00006. The genomes of these 213 CSSLs were resequenced and 580,524 single-nucleotide polymorphism markers were obtained, which were divided into 3,780 bin markers. The seed-pod-related traits were analyzed by quantitative trait locus (QTL) mapping using CSSLs. A total of 170 QTLs were detected, and 32 QTLs were detected stably for more than 2 years. Through epistasis analysis, 955 pairs of epistasis QTLs related to seed-pod traits were obtained. Furthermore, the hundred-seed weight QTL was finely mapped to the region of 64.4 Kb on chromosome 12, and Glyma.12G088900 was identified as a candidate gene. Taken together, a set of wild soybean CSSLs was constructed and upgraded by a resequencing technique. The seed-pod-related traits were studied by bin markers, and a candidate gene for the hundred-seed weight was finely mapped. Our results have revealed the CSSLs can be an effective tool for QTL mapping, epistatic effect analysis, and gene cloning.
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Affiliation(s)
| | - Lilong Hou
- Northeast Agricultural University, Harbin, China
| | - Jianguo Xie
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
| | - Fubin Cao
- Northeast Agricultural University, Harbin, China
| | - Ruru Wei
- Northeast Agricultural University, Harbin, China
| | | | - Zhaoming Qi
- Northeast Agricultural University, Harbin, China
| | | | | | - Dawei Xin
- Northeast Agricultural University, Harbin, China
| | - Candong Li
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Chunyan Liu
- Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, China
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25
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Renzi JP, Coyne CJ, Berger J, von Wettberg E, Nelson M, Ureta S, Hernández F, Smýkal P, Brus J. How Could the Use of Crop Wild Relatives in Breeding Increase the Adaptation of Crops to Marginal Environments? FRONTIERS IN PLANT SCIENCE 2022; 13:886162. [PMID: 35783966 PMCID: PMC9243378 DOI: 10.3389/fpls.2022.886162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/11/2022] [Indexed: 06/01/2023]
Abstract
Alongside the use of fertilizer and chemical control of weeds, pests, and diseases modern breeding has been very successful in generating cultivars that have increased agricultural production several fold in favorable environments. These typically homogeneous cultivars (either homozygous inbreds or hybrids derived from inbred parents) are bred under optimal field conditions and perform well when there is sufficient water and nutrients. However, such optimal conditions are rare globally; indeed, a large proportion of arable land could be considered marginal for agricultural production. Marginal agricultural land typically has poor fertility and/or shallow soil depth, is subject to soil erosion, and often occurs in semi-arid or saline environments. Moreover, these marginal environments are expected to expand with ongoing climate change and progressive degradation of soil and water resources globally. Crop wild relatives (CWRs), most often used in breeding as sources of biotic resistance, often also possess traits adapting them to marginal environments. Wild progenitors have been selected over the course of their evolutionary history to maintain their fitness under a diverse range of stresses. Conversely, modern breeding for broad adaptation has reduced genetic diversity and increased genetic vulnerability to biotic and abiotic challenges. There is potential to exploit genetic heterogeneity, as opposed to genetic uniformity, in breeding for the utilization of marginal lands. This review discusses the adaptive traits that could improve the performance of cultivars in marginal environments and breeding strategies to deploy them.
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Affiliation(s)
- Juan Pablo Renzi
- Instituto Nacional de Tecnología Agropecuaria, Hilario Ascasubi, Argentina
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | | | - Jens Berger
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
| | - Eric von Wettberg
- Department of Plant and Soil Science, Gund Institute for Environment, University of Vermont, Burlington, VT, United States
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Matthew Nelson
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Soledad Ureta
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Fernando Hernández
- CERZOS, Departamento de Agronomía, Universidad Nacional del Sur (CONICET), Bahía Blanca, Argentina
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, Olomouc, Czechia
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26
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Yang P, Sun X, Liu X, Wang W, Hao Y, Chen L, Liu J, He H, Zhang T, Bao W, Tang Y, He X, Ji M, Guo K, Liu D, Teng Z, Liu D, Zhang J, Zhang Z. Identification of Candidate Genes for Lint Percentage and Fiber Quality Through QTL Mapping and Transcriptome Analysis in an Allotetraploid Interspecific Cotton CSSLs Population. FRONTIERS IN PLANT SCIENCE 2022; 13:882051. [PMID: 35574150 PMCID: PMC9100888 DOI: 10.3389/fpls.2022.882051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Upland cotton (Gossypium hirsutum) has long been an important fiber crop, but the narrow genetic diversity of modern G. hirsutum limits the potential for simultaneous improvement of yield and fiber quality. It is an effective approach to broaden the genetic base of G. hirsutum through introgression of novel alleles from G. barbadense with excellent fiber quality. In the present study, an interspecific chromosome segment substitution lines (CSSLs) population was established using G. barbadense cultivar Pima S-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. A total of 105 quantitative trait loci (QTL), including 85 QTL for fiber quality and 20 QTL for lint percentage (LP), were identified based on phenotypic data collected from four environments. Among these QTL, 25 stable QTL were detected in two or more environments, including four for LP, eleven for fiber length (FL), three for fiber strength (FS), six for fiber micronaire (FM), and one for fiber elongation (FE). Eleven QTL clusters were observed on nine chromosomes, of which seven QTL clusters harbored stable QTL. Moreover, eleven major QTL for fiber quality were verified through analysis of introgressed segments of the eight superior lines with the best comprehensive phenotypes. A total of 586 putative candidate genes were identified for 25 stable QTL associated with lint percentage and fiber quality through transcriptome analysis. Furthermore, three candidate genes for FL, GH_A08G1681 (GhSCPL40), GH_A12G2328 (GhPBL19), and GH_D02G0370 (GhHSP22.7), and one candidate gene for FM, GH_D05G1346 (GhAPG), were identified through RNA-Seq and qRT-PCR analysis. These results lay the foundation for understanding the molecular regulatory mechanism of fiber development and provide valuable information for marker-assisted selection (MAS) in cotton breeding.
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27
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Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
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Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
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28
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Ding G, Hu B, Zhou Y, Yang W, Zhao M, Xie J, Zhang F. Development and Characterization of Chromosome Segment Substitution Lines Derived from Oryza rufipogon in the Background of the Oryza sativa indica Restorer Line R974. Genes (Basel) 2022; 13:genes13050735. [PMID: 35627119 PMCID: PMC9140843 DOI: 10.3390/genes13050735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/04/2022] Open
Abstract
Dongxiang wild rice (DXWR) (O. rufipogon Griff.), which has the northernmost worldwide distribution of a wild rice species, is a valuable genetic resource with respect to improving stress tolerance in cultivated rice (Oryza sativa L.). In the three-line hybrid rice breeding system, restorer lines play important roles in enhancing the tolerance of hybrid rice. However, restorer lines have yet to be used as a genomic background for development of substitution lines carrying DXWR chromosome segments. We developed a set of 84 chromosome segment substitution lines (CSSLs) from a donor parent DXWR × recurrent parent restorer line R974 (Oryza sativa indica) cross. On average, each CSSL carried 6.27 introgressed homozygous segments, with 93.37% total genome coverage. Using these CSSLs, we identified a single QTL, qDYST-1, associated with salt stress tolerance on chromosome 3. Furthermore, five CSSLs showing strong salt stress tolerance were subjected to whole-genome single-nucleotide polymorphism chip analyses, during which we detected a common substitution segment containing qDYST-1 in all five CSSLs, thereby implying the validity and efficacy of qDYST-1. These novel CSSLs could make a significant contribution to detecting valuable DXWR QTLs, and provide important germplasm resources for breeding novel restorer lines for use in hybrid rice breeding systems.
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Affiliation(s)
- Gumu Ding
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Biaolin Hu
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330022, China;
| | - Yi Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Wanling Yang
- Jiangxi Provincial Key Laboratory of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China;
| | - Minmin Zhao
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
| | - Jiankun Xie
- Jiangxi Provincial Key Laboratory of Protection and Utilization of Subtropical Plant Resources, Nanchang 330022, China;
- Correspondence: (J.X.); (F.Z.)
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.D.); (Y.Z.); (M.Z.)
- Correspondence: (J.X.); (F.Z.)
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29
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Sun S, Wang Z, Xiang S, Lv M, Zhou K, Li J, Liang P, Li M, Li R, Ling Y, He G, Zhao F. Identification, pyramid, and candidate gene of QTL for yield-related traits based on rice CSSLs in indica Xihui18 background. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:19. [PMID: 37309460 PMCID: PMC10248596 DOI: 10.1007/s11032-022-01284-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Chromosome segment substitution line (CSSL) is important for functional analysis and design breeding of target genes. Here, a novel rice CSSL-Z431 was identified from indica restorer line Xihui18 as recipient and japonica Huhan3 as donor. Z431 contained six segments from Huhan3, with average substitution length of 2.12 Mb. Compared with Xihui18, Z431 increased panicle number per plant (PN) and displayed short-wide grains. The short-wide grain of Z431 was caused by decreased length and increased width of glume cell. Then, thirteen QTLs were identified in secondary F2 population from Xihui18/Z431. Again, eleven QTLs (qPL3, qPN3, qGPP12, qSPP12, qGL3, qGW5, qRLW2, qRLW3, qRLW5, qGWT3, qGWT5-2) were validated by six single-segment substitution lines (SSSLs, S1-S6) developed in F3. In addition, fifteen QTLs (qPN5, qGL1, qGL2, qGL5, qGW1, qGW5-1, qRLW1, qRLW5-2, qGWT1, qGWT2, qYD1, qYD2, qYD3, qYD5, qYD12) were detected by these SSSLs, while not be identified in the F2 population. Multiple panicles of Z431 were controlled by qPN3 and qPN5. OsIAGLU should be the candidate gene for qPN3. The short-wide grain of Z431 was controlled by qGL3, qGW5, etc. By DNA sequencing and qRT-PCR analysis, two best candidate genes for qGL3 and qGW5 were identified, respectively. In addition, pyramid of different QTLs in D1-D3 and T1-T2 showed independent inheritance or various epistatic effects. So, it is necessary to understand all genetic effects of target QTLs for designing breeding. Furthermore, these secondary substitution lines improved the deficiencies of Xihui18 to some extent, especially increasing yield per plant in S1, S3, S5, D1-D3, T1, and T2. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01284-x.
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Affiliation(s)
- Shuangfei Sun
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Zongbing Wang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Siqian Xiang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Meng Lv
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Kai Zhou
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Juan Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Peixuan Liang
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Miaomiao Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Ruxiang Li
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Yinghua Ling
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Guanghua He
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
| | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Science,, Southwest University, Chongqing, 400715 People’s Republic of China
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30
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Han X, Li J, Zhao Y, Zhang Z, Jiang H, Wang J, Feng X, Zhang Y, Du Z, Wu X, Chen Q, Qi Z. Integrated transcriptomic and proteomic characterization of a chromosome segment substitution line reveals a new regulatory network controlling the seed storage profile of soybean. Food Energy Secur 2022. [DOI: 10.1002/fes3.381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Xue Han
- College of Agriculture Northeast Agricultural University Harbin China
- Heilongjiang Academy of Land Reclamation Sciences Harbin China
| | - Jiapeng Li
- College of Agriculture Northeast Agricultural University Harbin China
| | - Yabin Zhao
- College of Agriculture Northeast Agricultural University Harbin China
| | - Zhanguo Zhang
- College of Agriculture Northeast Agricultural University Harbin China
| | - Hongwei Jiang
- Soybean Research Institute Jilin Academy of Agricultural Sciences Changchun China
| | - Jinxing Wang
- Suihua Branch Institute, HeiLongJiang Academy of Agricultural Sciences Suihua China
| | - Xuezhen Feng
- College of Agriculture Northeast Agricultural University Harbin China
| | - Yu Zhang
- College of Agriculture Northeast Agricultural University Harbin China
| | - Ziyue Du
- College of Agriculture Northeast Agricultural University Harbin China
| | - Xiaoxia Wu
- College of Agriculture Northeast Agricultural University Harbin China
| | - Qingshan Chen
- College of Agriculture Northeast Agricultural University Harbin China
| | - Zhaoming Qi
- College of Agriculture Northeast Agricultural University Harbin China
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31
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Zhang Y, Zhou J, Xu P, Li J, Deng X, Deng W, Yang Y, Yu Y, Pu Q, Tao D. A Genetic Resource for Rice Improvement: Introgression Library of Agronomic Traits for All AA Genome Oryza Species. FRONTIERS IN PLANT SCIENCE 2022; 13:856514. [PMID: 35401612 PMCID: PMC8992386 DOI: 10.3389/fpls.2022.856514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/07/2022] [Indexed: 05/20/2023]
Abstract
Rice improvement depends on the availability of genetic variation, and AA genome Oryza species are the natural reservoir of favorable alleles that are useful for rice breeding. To systematically evaluate and utilize potentially valuable traits of new QTLs or genes for the Asian cultivated rice improvement from all AA genome Oryza species, 6,372 agronomic trait introgression lines (ILs) from BC2 to BC6 were screened and raised based on the variations in agronomic traits by crossing 170 accessions of 7 AA genome species and 160 upland rice accessions of O. sativa as the donor parents, with three elite cultivars of O. sativa, Dianjingyou 1 (a japonica variety), Yundao 1 (a japonica variety), and RD23 (an indica variety) as the recurrent parents, respectively. The agronomic traits, such as spreading panicle, erect panicle, dense panicle, lax panicle, awn, prostrate growth, plant height, pericarp color, kernel color, glabrous hull, grain size, 1,000-grain weight, drought resistance and aerobic adaption, and blast resistance, were derived from more than one species. Further, 1,401 agronomic trait ILs in the Dianjingyou 1 background were genotyped using 168 SSR markers distributed on the whole genome. A total of twenty-two novel allelic variations were identified to be highly related to the traits of grain length (GL) and grain width (GW), respectively. In addition, allelic variations for the same locus were detected from the different donor species, which suggest that these QTLs or genes were conserved and the different haplotypes of a QTL (gene) were valuable resources for broadening the genetic basis in Asian cultivated rice. Thus, this agronomic trait introgression library from multiple species and accessions provided a powerful resource for future rice improvement and genetic dissection of agronomic traits.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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Kalluri N, Serra O, Donoso JM, Picañol R, Howad W, Eduardo I, Arús P. Construction of a collection of introgression lines of "Texas" almond DNA fragments in the "Earlygold" peach genetic background. HORTICULTURE RESEARCH 2022; 9:uhac070. [PMID: 35669708 PMCID: PMC9157678 DOI: 10.1093/hr/uhac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/09/2022] [Indexed: 06/15/2023]
Abstract
Peach [Prunus persica L. Batsch] is one of the major temperate fruit tree species, the commercial materials of which have a low level of genetic variability. Almond [P. dulcis (Mill) DA Webb], a close relative of peach cultivated for its kernels, has a much higher level of diversity. The species are inter-compatible and often produce fertile hybrids, almond being a possible source of new genes for peach that could provide biotic and abiotic stress tolerance traits. In this paper we describe the development of a collection of peach-almond introgression lines (ILs) having a single fragment of almond (cv. Texas) in the peach background (cv. Earlygold). Lines with few introgressions were selected with markers from successive generations from a "Texas" × "Earlygold" F1 hybrid, initially using a set of SSRs and later with the 18 k peach SNP chip, allowing for the final extraction of 67 lines, 39 with almond heterozygous introgressions covering 99% of the genome, and 28 with homozygous introgressions covering 83% of the genome. As a proof of concept, four major genes and four quantitative characters were examined in the selected ILs giving results generally consistent with previous information on the genetics of these characters. This collection is the first of its kind produced in a woody perennial species and promises to be a valuable tool for genetic analyses, including dissection of quantitative traits, positional cloning, epistasis and as prebreeding material to introgress almond genes of interest into the peach commercial gene pool.
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Affiliation(s)
- Naveen Kalluri
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Octávio Serra
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Banco Português de Germoplasma Vegetal (BPGV), Braga, Portugal
| | - José Manuel Donoso
- Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Rayentué, Av. Salamanca s/n Sector Los Choapinos, Rengo 2940000, Chile
| | - Roger Picañol
- Rijk Zwaan Ibérica S.A. Finca La Marina-PJ Lo Contreras 30395, La Puebla|Cartagena (Murcia), Spain
| | - Werner Howad
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Fan J, Hua H, Luo Z, Zhang Q, Chen M, Gong J, Wei X, Huang Z, Huang X, Wang Q. Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice. RICE (NEW YORK, N.Y.) 2022; 15:5. [PMID: 35024991 PMCID: PMC8758858 DOI: 10.1186/s12284-022-00550-y] [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: 11/16/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Rice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitative trait locus (QTL) mapping in rice. Moreover, CSSLs containing target genomic regions can be used as improved varieties in rice breeding. In this study, we developed a set of CSSLs consisting of 117 lines derived from the recipient 'Huanghuazhan' (HHZ) and the donor 'Basmati Surkb 89-15' (BAS). The 117 lines were extensively genotyped by whole-genome resequencing, and a high-density genotype map was constructed for the CSSL population. The 117 CSSLs covered 99.78% of the BAS genome. Each line contained a single segment, and the average segment length was 6.02 Mb. Using the CSSL population, we investigated three agronomic traits in Shanghai and Hangzhou, China, and a total of 25 QTLs were detected in both environments. Among those QTLs, we found that RFT1 was the causal gene for heading date variance between HHZ and BAS. RFT1 from BAS was found to contain a loss-of-function allele based on yeast two-hybrid assay, and its causal variation was a P to S change in the 94th amino acid of the RFT1 protein. The combination of high-throughput genotyping and marker-assisted selection (MAS) is a highly efficient way to construct CSSLs in rice, and extensively genotyped CSSLs will be a powerful tool for the genetic mapping of agronomic traits and molecular breeding for target QTLs/genes.
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Affiliation(s)
- Jiongjiong Fan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Hua Hua
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Zhaowei Luo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Mengjiao Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Zonghua Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China.
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Tsugawa H, Rai A, Saito K, Nakabayashi R. Metabolomics and complementary techniques to investigate the plant phytochemical cosmos. Nat Prod Rep 2021; 38:1729-1759. [PMID: 34668509 DOI: 10.1039/d1np00014d] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.
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Affiliation(s)
- Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei, Tokyo 184-8588, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Amit Rai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Bohra A, Kilian B, Sivasankar S, Caccamo M, Mba C, McCouch SR, Varshney RK. Reap the crop wild relatives for breeding future crops. Trends Biotechnol 2021; 40:412-431. [PMID: 34629170 DOI: 10.1016/j.tibtech.2021.08.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023]
Abstract
Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), 208024 Kanpur, India
| | | | - Shoba Sivasankar
- International Atomic Energy Agency (IAEA), Vienna International Centre, 1400 Vienna, Austria
| | | | - Chikelu Mba
- Food and Agriculture Organization of the United Nations (FAO), Rome 00153, Italy
| | - Susan R McCouch
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA.
| | - Rajeev K Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia.
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Huang M, Qin R, Li C, Liu C, Jiang Y, Yu J, Chang D, Roberts PA, Chen Q, Wang C. Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents. THE PLANT GENOME 2021; 14:e20091. [PMID: 33817979 DOI: 10.1002/tpg2.20091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Chromosome segment substitution lines (CSSLs) are valuable genetic resources for quantitative trait loci (QTL) mapping of complex agronomic traits especially suitable for minor effect QTL. Here, 162 BC3 F7 -BC7 F3 CSSLs derived from crossing two susceptible parent lines, soybean [Glycine max (L.) Merr.] 'Suinong14' (recurrent parent) × wild soybean (G. soja Siebold & Zucc.) ZYD00006, were used for QTL mapping of soybean cyst nematode (SCN, Heterodera glycine Ichinohe) resistance based on female index (FI) and cysts per gram root (CGR) through phenotypic screening and whole-genome resequencing of CSSLs. Phenotypic results displayed a wide range of distribution and transgressive lines in both HG Type 2.5.7 FI and CGR and demonstrated a higher correlation between CGR and root weight (R2 = .5424) compared with than between FI and CGR (R2 = .0018). Using the single-marker analysis nonparametric mapping test, 33 significant QTL were detected on 18 chromosomes contributing resistance to FI and CGR. Fourteen QTL contributing 5.6-15.5% phenotypic variance (PVE) to FI were revealed on 11 chromosomes, and 16 QTL accounting for 6.1-36.2% PVE in CGR were detected on 14 chromosomes with strong additive effect by multiple-QTL model (MQM) mapping. Twenty-five and 13 out of all 38 QTL identified for FI and CGR on 20 chromosomes were from ZYD00006 and Suinong14, respectively. The CSSLs with the combination of positive alleles for FI, CGR, and root weight exhibited low nematode reproduction. For the first time, QTL associated with CGR have been detected, and both FI and CGR should be considered for breeding purposes in the absence of strong resistance genes such as rhg1 and Rhg4.
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Affiliation(s)
- Minghui Huang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruifeng Qin
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunjie Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
| | - Chunyan Liu
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Ye Jiang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinyao Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
| | - Doudou Chang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, 92521, USA
| | - Qingshan Chen
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Congli Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
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Wang D, Zhou K, Xiang S, Zhang Q, Li R, Li M, Liang P, Farkhanda N, He G, Ling Y, Zhao F. Identification, pyramid and candidate genes of QTLs for associated traits based on a dense erect panicle rice CSSL-Z749 and five SSSLs, three DSSLs and one TSSL. RICE (NEW YORK, N.Y.) 2021; 14:55. [PMID: 34132908 PMCID: PMC8208356 DOI: 10.1186/s12284-021-00496-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Seed-set density is an important agronomic trait in rice. However, its genetic mechanism is complex. Chromosome segment substitution lines (CSSLs) are ideal materials for studying complex traits. RESULTS A rice CSSL, Z749, with a dense and erect panicle phenotype, was identified among progeny of the recipient parent Nipponbare and the donor parent Xihui 18. Z749 carried seven substitution segments (average length 2.12 Mb). Compared with Nipponbare, Z749 showed significant increases in the numbers of primary (NPB) and secondary branches (NSB), number of spikelets (SPP) and grains per panicle (GPP), seed-set density (SSD), and decrease in panicle length (PL). A secondary F2 population derived from a cross between Nipponbare and Z749 was used to map quantitative trait loci (QTLs) for associated traits. Fifteen QTLs distributed on chromosomes 5, 7, 8, and 10 were detected. The QTL qPL7 might be an allele of OsFAD8 and the remaining 14 QTLs (e.g., qSSD5 and qSSD10 etc.) might be novel. Fourteen QTLs were verified using five single-segment substitution lines (SSSLs). The seed-set density of Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). The QTLs qSSD10, qSSD5, and qSSD8 were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, and 8, respectively. Analysis of QTL additive effects indicated that qSSD5, qSSD8, and qSSD10 from Xihui18 increased seed-set density of Z749 by 14.10, 11.38, and 5.11 spikelets per 10 cm panicle, respectively. Analysis of QTL epistatic effects revealed that pyramiding of qSSD5 and qSSD8, qSSD5 and qSSD10, qSSD8 and qSSD10, and qSSD5, qSSD8 and qSSD10 produced novel genotypes with increased seed-set density. CONCLUSIONS Inheritance of seed-set density in Z749 was controlled predominantly by one major QTL (qSSD10) and two minor QTLs (qSSD5 and qSSD8). Then, they were fine-mapped to intervals of 1.05, 1.46, and 1.53 Mb on chromosomes 10, 5, 8, respectively. Two MAPK genes (OsMPK9 and OsMPK17) and one gene (candidate gene 6) involved in auxin metabolism might be candidate genes for qSSD5, and OsSAUR32 might be the candidate gene for qSSD8. Pyramiding of qSSD5, qSSD8, and qSSD10 enhanced seed-set density.
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Affiliation(s)
- Dachuan Wang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Kai Zhou
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Siqian Xiang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Qiuli Zhang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Ruxiang Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Miaomiao Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Peixuan Liang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Naz Farkhanda
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Guanghua He
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Yinghua Ling
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China
| | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, 400715, Chongqing, PR China.
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Liang P, Wang H, Zhang Q, Zhou K, Li M, Li R, Xiang S, Zhang T, Ling Y, Yang Z, He G, Zhao F. Identification and Pyramiding of QTLs for Rice Grain Size Based on Short-Wide Grain CSSL-Z563 and Fine-Mapping of qGL3-2. RICE (NEW YORK, N.Y.) 2021; 14:35. [PMID: 33847838 PMCID: PMC8044274 DOI: 10.1186/s12284-021-00477-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/26/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Chromosome segment substitution lines (CSSLs) can be used to dissect complex traits, from which single-segment substitution lines (SSSLs) containing a target quantitative trait loci (QTL) can be developed, and they are thus important for functional analysis and molecular breeding. RESULTS A rice line with short wide grains, CSSL-Z563, was isolated from advanced-generation backcross population (BC3F6) derived from 'Xihui 18' (the recipient parent) and 'Huhan 3' (the donor parent). Z563 carried seven segments from 'Huhan 3', distributed on chromosomes 3, 7, and 8, with average substitution length of 5.52 Mb. Eleven QTLs for grain size were identified using secondary F2 population of 'Xihui 18'/Z563. The QTLs qGL3-1, qGL3-2, and qGL7 control grain length in Z563 and have additive effects to reduce grain length; qGW3-1 and qGW3-2 control grain width in Z563 and have additive effects to increase grain width. Four SSSLs, three double-segment substitution lines (D1-D3), and two triple-segment substitution lines (T1 and T2) were developed containing the target QTLs. The genetic stability of eight QTLs, including qGL3-2, qGL3-1, and qGL7, was verified by the SSSLs. D1 (containing qGL3-2 and qGL3-1), D2 (qGL3-1 and qGL7), and T1 (qGL3-2, qGL3-1, and qGL7) had positive epistatic effects on grain length, and their grain length was shorter than that of the corresponding SSSLs. The QTL qGL3-2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes that differed between 'Xihui 18' and Z563. These results are important for functional research on qGL3-2 and molecular breeding of hybrid rice cultivars. CONCLUSIONS The short and wide grain of Z563 was mainly controlled by qGL3-1, qGL3-2, qGL7, qGW3-1 and qGW3-2. The major QTL qGL3-2 was fine-mapped to a 696 Kb region of chromosome 3 containing five candidate genes. Different QTLs pyramiding displayed various phenotypes. In essence, the performance after pyramiding of genes depended on the comparison between the algebraic sum of the additive and epistatic effects of QTLs in the pyramidal line and the additive effect value of the single QTL. The results lay good foundation in the functional analysis of qGL3-2 and molecular design breeding of novel hybrid rice cultivars.
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Affiliation(s)
- Peixuan Liang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hui Wang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Qiuli Zhang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Kai Zhou
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Miaomiao Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ruxiang Li
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Siqian Xiang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Ting Zhang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yinghua Ling
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zhenglin Yang
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guanghua He
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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Calvo-Baltanás V, Wang J, Chae E. Hybrid Incompatibility of the Plant Immune System: An Opposite Force to Heterosis Equilibrating Hybrid Performances. FRONTIERS IN PLANT SCIENCE 2021; 11:576796. [PMID: 33717206 PMCID: PMC7953517 DOI: 10.3389/fpls.2020.576796] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
Hybridization is a core element in modern rice breeding as beneficial combinations of two parental genomes often result in the expression of heterosis. On the contrary, genetic incompatibility between parents can manifest as hybrid necrosis, which leads to tissue necrosis accompanied by compromised growth and/or reduced reproductive success. Genetic and molecular studies of hybrid necrosis in numerous plant species revealed that such self-destructing symptoms in most cases are attributed to autoimmunity: plant immune responses are inadvertently activated in the absence of pathogenic invasion. Autoimmunity in hybrids predominantly occurs due to a conflict involving a member of the major plant immune receptor family, the nucleotide-binding domain and leucine-rich repeat containing protein (NLR; formerly known as NBS-LRR). NLR genes are associated with disease resistance traits, and recent population datasets reveal tremendous diversity in this class of immune receptors. Cases of hybrid necrosis involving highly polymorphic NLRs as major causes suggest that diversified R gene repertoires found in different lineages would require a compatible immune match for hybridization, which is a prerequisite to ensure increased fitness in the resulting hybrids. In this review, we overview recent genetic and molecular findings on hybrid necrosis in multiple plant species to provide an insight on how the trade-off between growth and immunity is equilibrated to affect hybrid performances. We also revisit the cases of hybrid weakness in which immune system components are found or implicated to play a causative role. Based on our understanding on the trade-off, we propose that the immune system incompatibility in plants might play an opposite force to restrict the expression of heterosis in hybrids. The antagonism is illustrated under the plant fitness equilibrium, in which the two extremes lead to either hybrid necrosis or heterosis. Practical proposition from the equilibrium model is that breeding efforts for combining enhanced disease resistance and high yield shall be achieved by balancing the two forces. Reverse breeding toward utilizing genomic data centered on immune components is proposed as a strategy to generate elite hybrids with balanced immunity and growth.
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Identification of a novel QTL and candidate gene associated with grain size using chromosome segment substitution lines in rice. Sci Rep 2021; 11:189. [PMID: 33420305 PMCID: PMC7794494 DOI: 10.1038/s41598-020-80667-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Rice is one of the staple crops in the world. Grain size is an important determinant of rice grain yield, but the genetic basis of the grain size remains unclear. Here, we report a set of chromosome segment substitution lines (CSSL) developed in the genetic background of the genome-sequenced indica cultivar Zhenshan 97. Genotyping of the CSSLs by single nucleotide polymorphism array shows that most carry only one or two segments introduced from the genome-sequenced japonica cultivar Nipponbare. Using this population and the high-density markers, a total of 43 quantitative trait loci were identified for seven panicle- and grain-related traits. Among these loci, the novel locus qGL11 for grain length and thousand-grain weight was validated in a CSSL-derived segregating population and finely mapped to a 25-kb region that contains an IAA-amido synthetase gene OsGH3.13, This gene exhibited a significant expression difference in the young panicle between the near-isogenic lines that carry the contrasting Zhenshan 97 and Nipponbare alleles at qGL11. Expression and sequence analyses suggest that this gene is the most likely candidate for qGL11. Furthermore, several OsGH3.13 mutants induced by a CRISPR/Cas9 approach in either japonica or indica exhibit an increased grain length and thousand-grain weight, thus enhancing the final grain yield per plant. These findings provide insights into the genetic basis of grain size for the improvement of yield potential in rice breeding programs.
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Lin Y, Jiang X, Tao Y, Yang X, Wang Z, Wu F, Liu S, Li C, Deng M, Ma J, Chen G, Wei Y, Zheng Y, Liu Y. Identification and validation of stable quantitative trait loci for grain filling rate in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2377-2385. [PMID: 32430666 DOI: 10.1007/s00122-020-03605-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/09/2020] [Indexed: 05/19/2023]
Abstract
We identified and validated two stable grain filling rate (GFR) quantitative trait loci (QTL) in wheat that positively influenced several yield-related traits. Among them, QGfr.sicau-7D.1 was a novel GFR QTL. The grain filling rate (GFR) plays a crucial role in determining grain yield. To advance the current understanding of the genetic characteristics underlying the GFR in common wheat, three recombinant inbred line populations were used to map and validate GFR quantitative trait loci (QTL). Using a high-density genetic linkage map, 10 GFR QTL were detected. They were located on chromosomes 2D, 4A, 4B, 5B, 6D, 7A and 7D, explained 4.99-12.62% of the phenotypic variation. Two of them, QGfr.sicau-6D and QGfr.sicau-7D.1, were detected in all four environments tested and their genetic effect was validated by closely linked kompetitive allele specific PCR (KASP) markers in different genetic backgrounds. The effects of these two GFR QTL on other yield-related traits were also estimated. QGfr.sicau-6D had a significant positive influence (p < 0.01) on thousand kernel weight, kernel width, kernel volume, and kernel surface area. QGfr.sicau-7D.1 had a significant positive influence (p < 0.01) on thousand kernel weight and kernel length. Furthermore, QGfr.sicau-7D.1 was a completely novel QTL for GFR; several genes associated with grain growth and development were predicted in its physical interval. These results will facilitate molecular marker-assisted selection of wheat with high-confidence QTL for GFR and fine mapping of genes associated with GFR, thereby contributing to yield improvement.
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Affiliation(s)
- Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xiaojun Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yang Tao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Xilan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Zhiqiang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Fangkun Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shihang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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Shi Y, Liu A, Li J, Zhang J, Li S, Zhang J, Ma L, He R, Song W, Guo L, Lu Q, Xiang X, Gong W, Gong J, Ge Q, Shang H, Deng X, Pan J, Yuan Y. Examining two sets of introgression lines across multiple environments reveals background-independent and stably expressed quantitative trait loci of fiber quality in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2075-2093. [PMID: 32185421 PMCID: PMC7311500 DOI: 10.1007/s00122-020-03578-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/07/2020] [Indexed: 05/29/2023]
Abstract
Background-independent (BI) and stably expressed (SE) quantitative trait loci (QTLs) were identified using two sets of introgression lines across multiple environments. Genetic background more greatly affected fiber quality traits than environmental factors. Sixty-one SE-QTLs, including two BI-QTLs, were novel and 48 SE-QTLs, including seven BI-QTLs, were previously reported. Cotton fiber quality traits are controlled by QTLs and are susceptible to environmental influence. Fiber quality improvement is an essential goal in cotton breeding but is hindered by limited knowledge of the genetic basis of fiber quality traits. In this study, two sets of introgression lines of Gossypium hirsutum × G. barbadense were used to dissect the QTL stability of three fiber quality traits (fiber length, strength and micronaire) across environments using 551 simple sequence repeat markers selected from our high-density genetic map. A total of 76 and 120 QTLs were detected in the CCRI36 and CCRI45 backgrounds, respectively. Nine BI-QTLs were found, and 78 (41.71%) of the detected QTLs were reported previously. Thirty-nine and 79 QTLs were SE-QTLs in at least two environments in the CCRI36 and CCRI45 backgrounds, respectively. Forty-eight SE-QTLs, including seven BI-QTLs, were confirmed in previous reports, and 61 SE-QTLs, including two BI-QTLs, were considered novel. These results indicate that genetic background more strongly impacts on fiber quality traits than environmental factors. Twenty-three clusters with BI- and/or SE-QTLs were identified, 19 of which harbored favorable alleles from G. barbadense for two or three fiber quality traits. This study is the first report using two sets of introgression lines to identify fiber quality QTLs across environments in cotton, providing insights into the effect of genetic backgrounds and environments on the QTL expression of fiber quality and important information for the genetic basis underlying fiber quality traits toward QTL cloning and molecular breeding.
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Affiliation(s)
- Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Shaoqi Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinfeng Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liujun Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Rui He
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Weiwu Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lixue Guo
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Quanwei Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xianghui Xiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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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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Balakrishnan D, Surapaneni M, Yadavalli VR, Addanki KR, Mesapogu S, Beerelli K, Neelamraju S. Detecting CSSLs and yield QTLs with additive, epistatic and QTL×environment interaction effects from Oryza sativa × O. nivara IRGC81832 cross. Sci Rep 2020; 10:7766. [PMID: 32385410 PMCID: PMC7210974 DOI: 10.1038/s41598-020-64300-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/10/2020] [Indexed: 12/25/2022] Open
Abstract
Chromosome segment substitution lines (CSSLs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action and interaction in inter-specific crosses. In this study, a set of 90 back cross lines at BC2F8 generation derived from Swarna x Oryza nivara IRGC81832 was evaluated for yield traits under irrigated conditions in wet seasons of 3 consecutive years. We identified a set of 70 chromosome segment substitution lines, using genotyping data from 140 SSR markers covering 94.4% of O. nivara genome. Among these, 23 CSSLs were significantly different for 7 traits. 22 QTLs were detected for 11 traits with 6.51 to 46.77% phenotypic variation in 90 BILs. Three pleiotropic genomic regions associated with yield traits were mapped on chromosomes 1, 8 and 11. The marker interval RM206-RM144 at chromosome 11 was recurrently detected for various yield traits. Ten QTLs were identified consistently in the three consecutive years of testing. Seventeen pairs of significant epistatic QTLs (E-QTLs) were detected for days to flowering, days to maturity and plant height. Chromosome segments from O. nivara contributed trait enhancing alleles. The significantly improved lines and the stable QTLs identified in this study are valuable resource for gene discovery and yield improvement.
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Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10040467] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introgression lines (ILs) of eggplant (Solanum melongena) represent a resource of high value for breeding and the genetic analysis of important traits. We have conducted a phenotypic evaluation in two environments (open field and screenhouse) of 16 ILs from the first set of eggplant ILs developed so far. Each of the ILs carries a single marker-defined chromosomal segment from the wild eggplant relative S. incanum (accession MM577) in the genetic background of S. melongena (accession AN-S-26). Seventeen agronomic traits were scored to test the performance of ILs compared to the recurrent parent and of identifying QTLs for the investigated traits. Significant morphological differences were found between parents, and the hybrid was heterotic for vigour-related traits. Despite the presence of large introgressed fragments from a wild exotic parent, individual ILs did not display differences with respect to the recipient parent for most traits, although significant genotype × environment interaction (G × E ) was detected for most traits. Heritability values for the agronomic traits were generally low to moderate. A total of ten stable QTLs scattered across seven chromosomes was detected. For five QTLs, the S. incanum introgression was associated with higher mean values for plant- and flower-related traits, including vigour prickliness and stigma length. For one flower- and four fruit-related-trait QTLs, including flower peduncle and fruit pedicel lengths and fruit weight, the S. incanum introgression was associated with lower mean values for fruit-related traits. Evidence of synteny to other previously reported in eggplant populations was found for three of the fruit-related QTLs. The other seven stable QTLs are new, demonstrating that eggplant ILs are of great interest for eggplant breeding under different environments.
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Zhang H, Zhou L, Xu H, Wang L, Liu H, Zhang C, Li Q, Gu M, Wang C, Liu Q, Zhu Y. The qSAC3 locus from indica rice effectively increases amylose content under a variety of conditions. BMC PLANT BIOLOGY 2019; 19:275. [PMID: 31234778 PMCID: PMC6591921 DOI: 10.1186/s12870-019-1860-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/31/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Amylose content (AC) is a critical factor for the quality of rice. It is determined by the biosynthesis gene Waxy (Wx) and a variety of quantitative trait loci (QTLs). Although many QTLs have been reported to affect rice AC, few of them have been investigated under varying growth conditions, especially various temperatures, which are known to greatly influence the AC. RESULTS We analyzed the AC at different temperatures and planting seasons in a set of chromosome segment substitution lines (CSSLs) which were derived from a cross between the indica variety 9311 and the japonica variety Nipponbare carrying the same Wxb allele. A joint analysis detected a single locus, qSAC3, with a high logarithm of odds (LOD) score in four different conditions. The qSAC3 from indica 9311 (qSAC3ind) substantially increased the AC in japonica Nipponbare under all tested growth conditions. Furthermore, introducing the qSAC3ind into the soft rice variety Nangeng9108 with Wxmq, a mutant allele of Wxb, also moderately increased its AC and improved its appearance quality significantly by reducing the chalkiness of the polished rice. CONCLUSIONS Our results indicate that the qSAC3ind could increase the AC of japonica rice in different environments as well as in the background of different Wx alleles and that qSAC3 is a valuable locus for fine-tuning the rice AC and ameliorating the dull endosperm in rice varieties with the Wxmq allele.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Lihui Zhou
- Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Heng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Liangchao Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Huijie Liu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Cailin Wang
- Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Ying Zhu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
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