1
|
Song J, Liu K, Yang X, Chen Y, Xiong Y, Yang Q, Wang J, Zhang Z, Wu C, Wang J, Qiu L. QTL Mapping of Soybean ( Glycine max) Vine Growth Habit Trait. Int J Mol Sci 2023; 24:14770. [PMID: 37834218 PMCID: PMC10572949 DOI: 10.3390/ijms241914770] [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: 07/27/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The vine growth habit (VGH) is a notable property of wild soybean plants that also holds a high degree of importance in domestication as it can preclude using these wild cultivars for breeding and improving domesticated soybeans. Here, a bulked segregant analysis (BSA) approach was employed to study the genetic etiology of the VGH in soybean plants by integrating linkage mapping and population sequencing approaches. To develop a recombinant inbred line (RIL) population, the cultivated Zhongdou41 (ZD41) soybean cultivar was bred with ZYD02787, a wild soybean accession. The VGH status of each line in the resultant population was assessed, ultimately leading to the identification of six and nine QTLs from the BSA sequencing of the F4 population and F6-F8 population sequence mapping, respectively. One QTL shared across these analyzed generations was detected on chromosome 19. Three other QTLs detected by BSA-seq were validated and localized to the 90.93 kb, 2.9 Mb, and 602.08 kb regions of chromosomes 6 and 13, harboring 14, 53, and 4 genes, respectively. Three consistent VGH-related QTLs located on chromosomes 2 and 19 were detected in a minimum of three environments, while an additional six loci on chromosomes 2, 10, 13, and 18 were detected in at least two environments via ICIM mapping. Of all the detected loci, five had been reported previously whereas seven represent novel QTLs. Together, these data offer new insights into the genetic basis of the VGH in soybean plants, providing a rational basis to inform the use of wild accessions in future breeding efforts.
Collapse
Affiliation(s)
- Jian Song
- College of Life Science, Yangtze University, Jingzhou 434025, China; (J.S.); (C.W.)
| | - Kanglin Liu
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (K.L.); (X.Y.); (Y.C.); (Y.X.); (Q.Y.); (J.W.)
| | - Xuezhen Yang
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (K.L.); (X.Y.); (Y.C.); (Y.X.); (Q.Y.); (J.W.)
| | - Yijie Chen
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (K.L.); (X.Y.); (Y.C.); (Y.X.); (Q.Y.); (J.W.)
| | - Yajun Xiong
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (K.L.); (X.Y.); (Y.C.); (Y.X.); (Q.Y.); (J.W.)
| | - Qichao Yang
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (K.L.); (X.Y.); (Y.C.); (Y.X.); (Q.Y.); (J.W.)
| | - Jing Wang
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (K.L.); (X.Y.); (Y.C.); (Y.X.); (Q.Y.); (J.W.)
| | - Zhihao Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Caiyu Wu
- College of Life Science, Yangtze University, Jingzhou 434025, China; (J.S.); (C.W.)
| | - Jun Wang
- College of Agriculture, Yangtze University, Jingzhou 434025, China; (K.L.); (X.Y.); (Y.C.); (Y.X.); (Q.Y.); (J.W.)
| | - Lijuan Qiu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| |
Collapse
|
2
|
Jin T, Yin J, Wang T, Xue S, Li B, Zong T, Yang Y, Liu H, Liu M, Xu K, Wang L, Xing G, Zhi H, Li K. R SC3 K of soybean cv. Kefeng No.1 confers resistance to soybean mosaic virus by interacting with the viral protein P3. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:838-853. [PMID: 36330964 DOI: 10.1111/jipb.13401] [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: 09/06/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Soybean mosaic virus (SMV) is one of the most devastating viral pathogens of soybean (Glycine max (L.) Merr). In total, 22 Chinese SMV strains (SC1-SC22) have been classified based on the responses of 10 soybean cultivars to these pathogens. However, although several SMV-resistance loci in soybean have been identified, no gene conferring SMV resistance in the resistant soybean cultivar (cv.) Kefeng No.1 has been cloned and verified. Here, using F2 -derived F3 (F2:3 ) and recombinant inbred line (RIL) populations from a cross between Kefeng No.1 and susceptible soybean cv. Nannong 1138-2, we localized the gene in Kefeng No.1 that mediated resistance to SMV-SC3 strain to a 90-kb interval on chromosome 2. To study the functions of candidate genes in this interval, we performed Bean pod mottle virus (BPMV)-induced gene silencing (VIGS). We identified a recombinant gene (which we named RSC3 K) harboring an internal deletion of a genomic DNA fragment partially flanking the LOC100526921 and LOC100812666 reference genes as the SMV-SC3 resistance gene. By shuffling genes between infectious SMV DNA clones based on the avirulent isolate SC3 and virulent isolate 1129, we determined that the viral protein P3 is the avirulence determinant mediating SMV-SC3 resistance on Kefeng No.1. P3 interacts with RNase proteins encoded by RSC3 K, LOC100526921, and LOC100812666. The recombinant RSC3 K conveys much higher anti-SMV activity than LOC100526921 and LOC100812666, although those two genes also encode proteins that inhibit SMV accumulation, as revealed by gene silencing in a susceptible cultivar and by overexpression in Nicotiana benthamiana. These findings demonstrate that RSC3 K mediates the resistance of Kefeng No.1 to SMV-SC3 and that SMV resistance of soybean is determined by the antiviral activity of RNase proteins.
Collapse
Affiliation(s)
- Tongtong Jin
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinlong Yin
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Tao Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Song Xue
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bowen Li
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingxuan Zong
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunhua Yang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Liu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mengzhuo Liu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Liqun Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangnan Xing
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haijian Zhi
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai Li
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
3
|
Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
Collapse
Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
| |
Collapse
|
4
|
Jin T, Karthikeyan A, Wang L, Zong T, Wang T, Yin J, Hu T, Yang Y, Liu H, Cui Y, Zhao T, Zhi H. Digs out and characterization of the resistance gene accountable to soybean mosaic virus in soybean (Glycine max (L.) Merrill). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4217-4232. [PMID: 36114309 DOI: 10.1007/s00122-022-04213-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
A putative candidate gene conferring resistance to SMV strain SC1 was identified on chromosome 2, and the linked marker was validated in soybean cultivars Soybean mosaic, caused by the soybean mosaic virus, is the most common disease in soybean and a significant impediment to soybean production in the Huanghuai and Yangtze River regions of China. Kefeng No.1, a soybean cultivar, showed high resistance to soybean mosaic virus strain (SC1) collected from Huanghuai and Yangtze River regions. Genetic analysis based on the Mendelian genic population derived from the cross Kefeng No.1 × Nannong 1138-2 revealed that Kefeng No.1 possesses a single dominant gene. Furthermore, genetic fine-mapping using an F2 population containing 281 individuals delimited resistant gene to a genomic region of 186 kb flanked by SSR markers BS020610 and BS020620 on chromosome 2. Within this region, there were 14 genes based on the Williams 82 reference genome. According to sequence analysis, six of the 14 genes have amino acid differences, and one of these genes is the Rsv4 allele designated as Rsc1-DR. The functional analysis of candidate genes using the bean pod mottle virus (BPMV)-induced gene silencing (VIGS) system revealed that Rsc1-DR was accountable for Kefeng No.1's resistance to SMV-SC1. Based on the genome sequence of Rsc1-DR, an Insertion/Deletion (InDel) molecular marker, JT0212, was developed and genotyped using 100 soybean cultivars, and the coincidence rate was 89%. The study enriched our understanding of the SMV resistance mechanism. The marker developed in this study could be directly used by the soybean breeders to select the genotypes with favorable alleles for making crosses, and also it will facilitate marker-assisted selection of SMV resistance in soybean breeding.
Collapse
Affiliation(s)
- Tongtong Jin
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Adhimoolam Karthikeyan
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, 63243, South Korea
| | - Liqun Wang
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingxuan Zong
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Wang
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinlong Yin
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Hu
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunhua Yang
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Liu
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongchun Cui
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tuanjie Zhao
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Haijian Zhi
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean-Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
5
|
Lu Y, Zhang J, Guo X, Chen J, Chang R, Guan R, Qiu L. Identification of Genomic Regions Associated with Vine Growth and Plant Height of Soybean. Int J Mol Sci 2022; 23:5823. [PMID: 35628633 PMCID: PMC9146324 DOI: 10.3390/ijms23105823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/09/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Vining growth (VG) and high plant height (PH) are the physiological traits of wild soybean that preclude their utilization for domesticated soybean breeding and improvement. To identify VG- and PH-related quantitative trait loci (QTLs) in different genetic resources, two populations of recombinant inbred lines (RILs) were developed by crossing a cultivated soybean, Zhonghuang39 (ZH39), with two wild soybean accessions, NY27-38 and NY36-87. Each line from the two crosses was evaluated for VG and PH. Three QTLs for VG and three for PH, detected in the ZH39 × NY27-38 population of the RILs, co-located on chromosomes 2, 17 and 19. The VG- and PH-related QTL in the ZH39 × NY36-87 population co-located on chromosome 19. A common QTL shared by the two populations was located on chromosome 19, suggesting that this major QTL was consistently selected for in different genetic backgrounds. The results suggest that different loci are involved in the domestication or adaptations of soybean of various genetic backgrounds. The molecular markers presented here would benefit the fine mapping and cloning of candidate genes underlying the VG and PH co-localized regions and thus facilitate the utilization of wild resources in breeding by avoiding undesirable traits.
Collapse
Affiliation(s)
| | | | | | | | | | - Rongxia Guan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.L.); (J.Z.); (X.G.); (J.C.); (R.C.)
| | - Lijuan Qiu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.L.); (J.Z.); (X.G.); (J.C.); (R.C.)
| |
Collapse
|