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Zhang L, Duan Y, Zhang Z, Zhang L, Chen S, Cai C, Duan S, Zhang K, Li G, Cheng F. OcBSA: An NGS-based bulk segregant analysis tool for outcross populations. MOLECULAR PLANT 2024; 17:648-657. [PMID: 38369755 DOI: 10.1016/j.molp.2024.02.011] [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: 01/28/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Constructing inbred lines for self-incompatible species and species with long generation times is challenging, making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species. However, there is a lack of dedicated algorithms/tools for rapid quantitative trait locus (QTL) mapping using the F1 populations. To this end, we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population. Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy. In addition, the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple, pear, peach, citrus, grape, tea, and rice. We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study. The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene, which regulates potato flower color. Taken together, these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species. For ease of use, we have developed both Windows and Linux versions of OcBSA, which are freely available at: https://gitee.com/Bioinformaticslab/OcBSA.
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Affiliation(s)
- Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfeng Duan
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zewei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengcheng Cai
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoguang Duan
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangcun Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Tian Z, Wu B, Liu J, Zhang L, Wu T, Wang Y, Han Z, Zhang X. Genetic variations in MdSAUR36 participate in the negative regulation of mesocarp cell division and fruit size in Malus species. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:1. [PMID: 38222974 PMCID: PMC10784262 DOI: 10.1007/s11032-024-01441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/06/2023] [Indexed: 01/16/2024]
Abstract
Final fruit size of apple (Malus domestica) cultivars is related to both mesocarp cell division and cell expansion during fruit growth, but it is unclear whether the cell division and/or cell enlargement determine most of the differences in fruit size between Malus species. In this study, by using an interspecific hybrid population between Malus asiatica "Zisai Pearl" and Malus domestica cultivar "Red Fuji," we found that the mesocarp cell number was the main causal factor of diversity in fruit size between Malus species. Rapid increase in mesocarp cell number occurred prior to 28 days after anthesis (DAA), while cell size increased gradually after 28 DAA until fruit ripening. Six candidate genes related to auxin signaling or cell cycle were predicted by combining the RNA-seq data and previous QTL data for fruit weight. Two InDels and 10 SNPs in the promoter of a small auxin upregulated RNA gene MdSAUR36 in Zisai Pearl led to a lower promoter activity than that of Red Fuji. One non-synonymous SNP G/T at 379 bp downstream of the ATG codon of MdSAUR36, which was heterozygous in Zisai Pearl, exerted significant genotype effects on fruit weight, length, and width. Transgenic apple calli by over-expressing or RNAi MdSAUR36 confirmed that MdSAUR36 participated in the negative regulation of mesocarp cell division and thus apple fruit size. These results could provide new insights in the molecular mechanism of small fruit size in Malus accession and be potentially used in molecular assisted breeding via interspecific hybridization. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01441-4.
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Affiliation(s)
- Zhendong Tian
- College of Horticulture, China Agricultural University, Beijing, China
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jing Liu
- College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
| | - Libo Zhang
- Zhongbaolvdu Agricultural Research Centre, Beidaihe, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
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Shen F, Xu S, Shen Q, Bi C, Lysak MA. The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits. Nat Commun 2023; 14:4102. [PMID: 37491530 PMCID: PMC10368706 DOI: 10.1038/s41467-023-39800-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/29/2023] [Indexed: 07/27/2023] Open
Abstract
Polyploidization can provide a wealth of genetic variation for adaptive evolution and speciation, but understanding the mechanisms of subgenome evolution as well as its dynamics and ultimate consequences remains elusive. Here, we report the telomere-to-telomere (T2T) gap-free reference genome of allotetraploid horseradish (Armoracia rusticana) sequenced using a comprehensive strategy. The (epi)genomic architecture and 3D chromatin structure of the A and B subgenomes differ significantly, suggesting that both the dynamics of the dominant long terminal repeat retrotransposons and DNA methylation have played critical roles in subgenome diversification. Investigation of the genetic basis of biosynthesis of glucosinolates (GSLs) and horseradish peroxidases reveals both the important role of polyploidization and subgenome differentiation in shaping the key traits. Continuous duplication and divergence of essential genes of GSL biosynthesis (e.g., FMOGS-OX, IGMT, and GH1 gene family) contribute to the broad GSL profile in horseradish. Overall, the T2T assembly of the allotetraploid horseradish genome expands our understanding of polyploid genome evolution and provides a fundamental genetic resource for breeding and genetic improvement of horseradish.
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Affiliation(s)
- Fei Shen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Shixiao Xu
- Tobacco College, Henan Agricultural University, Zhengzhou, Henan, China
| | - Qi Shen
- Genome Research Center, Leeuwenhoek Biotechnology Inc., Hong Kong, China
- Shangji Biotechnology Inc., Tianjin, China
- PheniX, Plant Phenomics Research Centre, Nanjing Agricultural University, Nanjing, China
| | - Changwei Bi
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Martin A Lysak
- Central European Institute of Technology and National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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Yang X, Wu B, Liu J, Zhang Z, Wang X, Zhang H, Ren X, Zhang X, Wang Y, Wu T, Xu X, Han Z, Zhang X. A single QTL harboring multiple genetic variations leads to complicated phenotypic segregation in apple flesh firmness and crispness. PLANT CELL REPORTS 2022; 41:2379-2391. [PMID: 36208306 DOI: 10.1007/s00299-022-02929-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Within a QTL, the genetic recombination and interactions among five and two functional variations at MdbHLH25 and MdWDR5A caused much complicated phenotype segregation in apple FFR and FCR. The storability of climacteric fruit like apple is a quantitative trait. We previously identified 62 quantitative trait loci (QTLs) associating flesh firmness retainability (FFR) and flesh crispness retainability (FCR), but only a few functional genetic variations were identified and validated. The genetic variation network controlling fruit storability is far to be understood and diagnostic markers are needed for molecular breeding. We previously identified overlapped QTLs F16.1/H16.2 for FFR and FCR using an F1 population derived from 'Zisai Pearl' × 'Red Fuji'. In this study, five and two single-nucleotide polymorphisms (SNPs) were identified on the candidate genes MdbHLH25 and MdWDR5A within the QTL region. The SNP1 A allele at MdbHLH25 promoter reduced the expression and SNP2 T allele and/or SNP4/5 GT alleles at the exons attenuated the function of MdbHLH25 by downregulating the expression of the target genes MdACS1, which in turn led to a reduction in ethylene production and maintenance of higher flesh crispness. The SNPs did not alter the protein-protein interaction between MdbHLH25 and MdWDR5A. The joint effect of SNP genotype combinations by the SNPs on MdbHLH25 (SNP1, SNP2, and SNP4) and MdWDR5A (SNPi and SNPii) led to a much broad spectrum of phenotypic segregation in FFR and FCR. Together, the dissection of these genetic variations contributes to understanding the complicated effects of a QTL and provides good potential for marker development in molecular breeding.
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Affiliation(s)
- Xianglong Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jing Liu
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Zhongyan Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuan Wang
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Haie Zhang
- College of Horticultural Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xuejun Ren
- Testing and Analysis Center, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China.
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