How to select favorable and promising alleles and genotypes for breeding: A case study of rice blast resistance genes in Southern and Northeastern China
Asian rice comprises two major subspecies: Xian (X) and Geng (G), and the diverged resistance genes (R) have provided a foundation for breeding improved cultivars to control rice blast disease. After conducting two-phase allele mining using six updated FNP marker systems, the functional haplotypes a...
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KeAi Communications Co., Ltd.
2025-02-01
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| Series: | Crop Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214514125000029 |
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| author | Xing Wang Jinyan Wang Yaling Zhang Yongxiang Yao Ying Sun Liping Lin Xuemei Ye Rongbai Li Zhibin Liang Yizhen Deng Qinghua Pan |
| author_facet | Xing Wang Jinyan Wang Yaling Zhang Yongxiang Yao Ying Sun Liping Lin Xuemei Ye Rongbai Li Zhibin Liang Yizhen Deng Qinghua Pan |
| author_sort | Xing Wang |
| collection | DOAJ |
| description | Asian rice comprises two major subspecies: Xian (X) and Geng (G), and the diverged resistance genes (R) have provided a foundation for breeding improved cultivars to control rice blast disease. After conducting two-phase allele mining using six updated FNP marker systems, the functional haplotypes at Pit, Pib, and Pi63 strictly diverged into the X-populations and were defined as X-R loci, while those at Pi54, Pi37, and Pi36 into the G-populations as G-R loci. The genic diversity at the three X-R loci (16 alleles) was twofold higher than that at the three G-R loci (8 alleles), and the allelic diversity in the Southern region (21 alleles) was nearly double that in the Northeastern region (11 alleles). Both observations reflect a significant difference in genetic diversity between X- and G-populations, and indicate that the effective R-genes mainly originated from X-subspecies. Based on the allelic structures characterized by a set of 10 parameters, 8 and 16 alleles were respectively recognized as favorable and promising ones for the regional breeding programs. The genotypic structures of the two regional populations were almost different, indicating that the diverged alleles have been further assembled into two series of regional genotypes through long-term breeding programs, despite the presence of one-third of region-common alleles. The genotypic diversity in the Southern region (55 genotypes) was nearly twice as high as that in the Northeastern region (28), which perfectly reflects the aforementioned differences in both genic and allelic diversities. After analyzing the genotypic structures using a set of 13 parameters, 4 and 23 genotypes, respectively, can be recommended as the favorable and promising ones for the regional breeding programs. The case study serves as a concrete sample of how to identify the favorable and promising alleles and genotypes, and beneficial parents based their comprehensive population structures for gene-designed breeding. |
| format | Article |
| id | doaj-art-ea93a1a2db564420af242b8b2685d3c3 |
| institution | DOAJ |
| issn | 2214-5141 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Crop Journal |
| spelling | doaj-art-ea93a1a2db564420af242b8b2685d3c32025-08-20T03:16:18ZengKeAi Communications Co., Ltd.Crop Journal2214-51412025-02-0113110411410.1016/j.cj.2024.12.011How to select favorable and promising alleles and genotypes for breeding: A case study of rice blast resistance genes in Southern and Northeastern ChinaXing Wang0Jinyan Wang1Yaling Zhang2Yongxiang Yao3Ying Sun4Liping Lin5Xuemei Ye6Rongbai Li7Zhibin Liang8Yizhen Deng9Qinghua Pan10Rice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, China; Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, China; College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, China; Dandong Academy of Agricultural Sciences, Dandong 118109, Liaoning, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, ChinaCollege of Agriculture, Guangxi University, Nanning 510642, Guangxi, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, China; Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, China; Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, ChinaRice Blast Research Center, South China Agricultural University, Guangzhou 510642, Guangdong, China; Corresponding author.Asian rice comprises two major subspecies: Xian (X) and Geng (G), and the diverged resistance genes (R) have provided a foundation for breeding improved cultivars to control rice blast disease. After conducting two-phase allele mining using six updated FNP marker systems, the functional haplotypes at Pit, Pib, and Pi63 strictly diverged into the X-populations and were defined as X-R loci, while those at Pi54, Pi37, and Pi36 into the G-populations as G-R loci. The genic diversity at the three X-R loci (16 alleles) was twofold higher than that at the three G-R loci (8 alleles), and the allelic diversity in the Southern region (21 alleles) was nearly double that in the Northeastern region (11 alleles). Both observations reflect a significant difference in genetic diversity between X- and G-populations, and indicate that the effective R-genes mainly originated from X-subspecies. Based on the allelic structures characterized by a set of 10 parameters, 8 and 16 alleles were respectively recognized as favorable and promising ones for the regional breeding programs. The genotypic structures of the two regional populations were almost different, indicating that the diverged alleles have been further assembled into two series of regional genotypes through long-term breeding programs, despite the presence of one-third of region-common alleles. The genotypic diversity in the Southern region (55 genotypes) was nearly twice as high as that in the Northeastern region (28), which perfectly reflects the aforementioned differences in both genic and allelic diversities. After analyzing the genotypic structures using a set of 13 parameters, 4 and 23 genotypes, respectively, can be recommended as the favorable and promising ones for the regional breeding programs. The case study serves as a concrete sample of how to identify the favorable and promising alleles and genotypes, and beneficial parents based their comprehensive population structures for gene-designed breeding.http://www.sciencedirect.com/science/article/pii/S2214514125000029Rice blastXian and Geng type resistance genesAllelic and genotypic population structuresFavorable allele and genotypePromising allele and genotype |
| spellingShingle | Xing Wang Jinyan Wang Yaling Zhang Yongxiang Yao Ying Sun Liping Lin Xuemei Ye Rongbai Li Zhibin Liang Yizhen Deng Qinghua Pan How to select favorable and promising alleles and genotypes for breeding: A case study of rice blast resistance genes in Southern and Northeastern China Crop Journal Rice blast Xian and Geng type resistance genes Allelic and genotypic population structures Favorable allele and genotype Promising allele and genotype |
| title | How to select favorable and promising alleles and genotypes for breeding: A case study of rice blast resistance genes in Southern and Northeastern China |
| title_full | How to select favorable and promising alleles and genotypes for breeding: A case study of rice blast resistance genes in Southern and Northeastern China |
| title_fullStr | How to select favorable and promising alleles and genotypes for breeding: A case study of rice blast resistance genes in Southern and Northeastern China |
| title_full_unstemmed | How to select favorable and promising alleles and genotypes for breeding: A case study of rice blast resistance genes in Southern and Northeastern China |
| title_short | How to select favorable and promising alleles and genotypes for breeding: A case study of rice blast resistance genes in Southern and Northeastern China |
| title_sort | how to select favorable and promising alleles and genotypes for breeding a case study of rice blast resistance genes in southern and northeastern china |
| topic | Rice blast Xian and Geng type resistance genes Allelic and genotypic population structures Favorable allele and genotype Promising allele and genotype |
| url | http://www.sciencedirect.com/science/article/pii/S2214514125000029 |
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