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Sivabharathi RC, Rajagopalan VR, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M. Haplotype-based breeding: A new insight in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024:112129. [PMID: 38763472 DOI: 10.1016/j.plantsci.2024.112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.
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Affiliation(s)
- R C Sivabharathi
- Department of Genetics and Plant breeding, CPBG, Tamil Nadu Agricultural University, Coimbatore - 641 003
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore -641 003
| | - R Suresh
- Department of Rice, CPBG, Tamil Nadu Agricultural University, Coimbatore -641 003
| | - M Sudha
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore -641 003.
| | - G Karthikeyan
- Department of Plant Pathology, CPPS, Tamil Nadu Agricultural University, Coimbatore -641 003
| | - M Jayakanthan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore -641 003
| | - M Raveendran
- Directorate of research, Tamil Nadu Agricultural University, Coimbatore -641 003.
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Du M, Jiang Z, Wang C, Wei C, Li Q, Cong R, Wang W, Zhang G, Li L. Genome-Wide Association Analysis of Heat Tolerance in F 2 Progeny from the Hybridization between Two Congeneric Oyster Species. Int J Mol Sci 2023; 25:125. [PMID: 38203295 PMCID: PMC10778899 DOI: 10.3390/ijms25010125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
As the world's largest farmed marine animal, oysters have enormous economic and ecological value. However, mass summer mortality caused by high temperature poses a significant threat to the oyster industry. To investigate the molecular mechanisms underlying heat adaptation and improve the heat tolerance ability in the oyster, we conducted genome-wide association analysis (GWAS) analysis on the F2 generation derived from the hybridization of relatively heat-tolerant Crassostrea angulata ♀ and heat-sensitive Crassostrea gigas ♂, which are the dominant cultured species in southern and northern China, respectively. Acute heat stress experiment (semi-lethal temperature 42 °C) demonstrated that the F2 population showed differentiation in heat tolerance, leading to extremely differentiated individuals (approximately 20% of individuals die within the first four days with 10% survival after 14 days). Genome resequencing and GWAS of the two divergent groups had identified 18 significant SNPs associated with heat tolerance, with 26 candidate genes located near these SNPs. Eleven candidate genes that may associate with the thermal resistance were identified, which were classified into five categories: temperature sensor (Trpm2), transcriptional factor (Gata3), protein ubiquitination (Ube2h, Usp50, Uchl3), heat shock subfamily (Dnajc17, Dnaja1), and transporters (Slc16a9, Slc16a14, Slc16a9, Slc16a2). The expressional differentiation of the above genes between C. gigas and C. angulata under sublethal temperature (37 °C) further supports their crucial role in coping with high temperature. Our results will contribute to understanding the molecular mechanisms underlying heat tolerance, and provide genetic markers for heat-resistance breeding in the oyster industry.
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Affiliation(s)
- Mingyang Du
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Zhuxiang Jiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chaogang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chenchen Wei
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
| | - Qingyuan Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Rihao Cong
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266100, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266100, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Wuhan 430072, China
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.D.); (Z.J.); (C.W.); (C.W.); (Q.L.); (R.C.); (W.W.); (G.Z.)
- University of Chinese Academy of Sciences, Beijing 101408, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266100, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Wuhan 430072, China
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