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Luo Z. Mapping quantitative trait loci in autotetraploids under a genuine tetrasomic model. New Phytol 2024; 242:21-22. [PMID: 38359878 DOI: 10.1111/nph.19597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Affiliation(s)
- Zewei Luo
- Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, 200433, China
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Cai Y, Zhou X, Wang C, Liu A, Sun Z, Li S, Shi X, Yang S, Guan Y, Cheng J, Wu Y, Qin R, Sun H, Zhao C, Li J, Cui F. Quantitative trait loci detection for three tiller-related traits and the effects on wheat (Triticum aestivum L.) yields. Theor Appl Genet 2024; 137:87. [PMID: 38512468 DOI: 10.1007/s00122-024-04589-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
KEY MESSAGE A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for tiller-related traits were reported, and the candidate genes underlying qMtn-KJ-5D, a novel major and stable QTL for maximum tiller number, were characterized. Tiller-related traits play an important role in determining the yield potential of wheat. Therefore, it is important to elucidate the genetic basis for tiller number when attempting to use genetic improvement as a tool for enhancing wheat yields. In this study, a quantitative trait locus (QTL) analysis of three tiller-related traits was performed on the recombinant inbred lines (RILs) of a mapping population, referred to as KJ-RILs, that was derived from a cross between the Kenong 9204 (KN9204) and Jing 411 (J411) lines. A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for spike number per plant (SNPP), maximum tiller number (MTN), and ear-bearing tiller rate (EBTR) were detected in eight different environments. Among these QTLs with additive effects, three major and stable QTLs were first documented herein. Almost all but two pairwise epistatic QTLs showed minor interaction effects accounting for no more than 3.0% of the phenotypic variance. The genetic effects of two colocated major and stable QTLs, i.e., qSnpp-KJ-5D.1 and qMtn-KJ-5D, for yield-related traits were characterized. The breeding selection effect of the beneficial allele for the two QTLs was characterized, and its genetic effects on yield-related traits were evaluated. The candidate genes underlying qMtn-KJ-5D were predicted based on multi-omics data, and TraesKN5D01HG00080 was identified as a likely candidate gene. Overall, our results will help elucidate the genetic architecture of tiller-related traits and can be used to develop novel wheat varieties with high yields.
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Affiliation(s)
- Yibiao Cai
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Xiaohan Zhou
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Chenyang Wang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Aifeng Liu
- Crop Research Institute, Shandong Academy of Agricultural Science, Jinan, 250100, People's Republic of China
| | - Zhencang Sun
- Jingbo Agrochemicals Technology Co., Ltd., Binzhou, 256500, People's Republic of China
| | - Shihui Li
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Xinyao Shi
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Shuang Yang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Yuxiang Guan
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Jiajia Cheng
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Yongzhen Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Ran Qin
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Han Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Chunhua Zhao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China.
| | - Junming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China.
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China.
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Jiang Y, Dong L, Li H, Liu Y, Wang X, Liu G. Genetic linkage map construction and QTL analysis for plant height in proso millet (Panicum miliaceum L.). Theor Appl Genet 2024; 137:78. [PMID: 38466414 DOI: 10.1007/s00122-024-04576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024]
Abstract
KEY MESSAGE A genetic linkage map representing proso millet genome was constructed with SSR markers, and a major QTL corresponding to plant height was mapped on chromosome 14 of this map. Proso millet (Panicum miliaceum L.) has the lowest water requirements of all cultivated cereal crops. However, the lack of a genetic map and the paucity of genomic resources for this species have limited the utility of proso millet for detailed genetic studies and hampered genetic improvement programs. In this study, 97,317 simple sequence repeat (SSR) markers were developed based on the genome sequence of the proso millet landrace Longmi 4. Using some of these markers in conjunction with previously identified SSRs, an SSR-based linkage map for proso millet was successfully constructed using a large mapping population (316 F2 offspring). In total, 186 SSR markers were assigned to 18 linkage groups corresponding to the haploid chromosomes. The constructed map had a total length of 3033.42 centimorgan (cM) covering 78.17% of the assembled reference genome. The length of the 18 linkage groups ranged from 88.89 cM (Chr. 15) to 274.82 cM (Chr. 16), with an average size of 168.17 cM. To our knowledge, this is the first genetic linkage map for proso millet based on SSR markers. Plant height is one of the most important traits in crop improvement. A major QTL was repeatedly detected in different environments, explaining 8.70-24.50% of the plant height variations. A candidate gene affecting auxin biosynthesis and transport, and ROS homeostasis regulation was predicted. Thus, the linkage map and QTL analysis provided herein will promote the development of gene mining and molecular breeding in proso millet.
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Affiliation(s)
- Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Li Dong
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yanan Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Xindong Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China.
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China.
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Zhao B, Li K, Wang M, Liu Z, Yin P, Wang W, Li Z, Li X, Zhang L, Han Y, Li J, Yang X. Genetic basis of maize stalk strength decoded via linkage and association mapping. Plant J 2024; 117:1558-1573. [PMID: 38113320 DOI: 10.1111/tpj.16583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/21/2023]
Abstract
Stalk lodging is a severe problem that limits maize production worldwide, although little attention has been given to its genetic basis. Here we measured rind penetrometer resistance (RPR), an effective index for stalk lodging, in a multi-parent population of 1948 recombinant inbred lines (RILs) and an association population of 508 inbred lines (AMP508). Linkage and association mapping identified 53 and 29 single quantitative trait loci (QTLs) and 50 and 19 pairs of epistatic interactions for RPR in the multi-parent population and AMP508 population, respectively. Phenotypic variation explained by all identified epistatic QTLs (up to ~5%) was much less than that explained by all single additive QTLs (up to ~33% in the multi-parent population and ~ 60% in the AMP508 population). Among all detected QTLs, only eight single QTLs explained >10% of phenotypic variation in single RIL populations. Alleles that increased RPR were enriched in tropical/subtropical (TST) groups from the AMP508 population. Based on genome-wide association studies in both populations, we identified 137 candidate genes affecting RPR, which were assigned to multiple biological processes, such as the biosynthesis of cell wall components. Sixty-six candidate genes were cross-validated by multiple methods or populations. Most importantly, 23 candidate genes were upregulated or downregulated in high-RPR lines relative to low-RPR lines, supporting the associations between candidate genes and RPR. These findings reveal the complex nature of the genetic basis underlying RPR and provide loci or candidate genes for developing elite varieties that are resistant to stalk lodging via molecular breeding.
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Affiliation(s)
- Binghao Zhao
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Kun Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Min Wang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Zhiyuan Liu
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Pengfei Yin
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Weidong Wang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Zhigang Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Xiaowei Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Lili Zhang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Yingjia Han
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Jiansheng Li
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience and National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, 100193, China
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Torrey EF. Did the human genome project affect research on Schizophrenia? Psychiatry Res 2024; 333:115691. [PMID: 38219345 DOI: 10.1016/j.psychres.2023.115691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
The Human Genome Project was undertaken primarily to discover genetic causes and better treatments for human diseases. Schizophrenia was targeted since three of the project`s principal architects had a personal interest and also because, based on family, adoption, and twin studies, schizophrenia was widely believed to be a genetic disorder. Extensive studies using linkage analysis, candidate genes, genome wide association studies [GWAS], copy number variants, exome sequencing and other approaches have failed to identify causal genes. Instead, they identified almost 300 single nucleotide polymorphisms [SNPs] associated with altered risks of developing schizophrenia as well as some rare variants associated with increased risk in a small number of individuals. Risk genes play a role in the clinical expression of most diseases but do not cause the disease in the absence of other factors. Increasingly, observers question whether schizophrenia is strictly a genetic disorder. Beginning in 1996 NIMH began shifting its research resources from clinical studies to basic research based on the promise of the Human Genome Project. Consequently, three decades later NIMH's genetics investment has yielded almost nothing clinically useful for individuals currently affected. It is time to review NIMH`s schizophrenia research portfolio.
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Naik S, Sudan J, Urwat U, Pakhtoon MM, Bhat B, Sharma V, Sofi PA, Shikari AB, Bhat BA, Sofi NR, Prasad PVV, Zargar SM. Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat. Plant Genome 2024; 17:e20427. [PMID: 38239091 DOI: 10.1002/tpg2.20427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/07/2023] [Accepted: 12/22/2023] [Indexed: 03/22/2024]
Abstract
Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker-trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.
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Affiliation(s)
- Samiullah Naik
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jebi Sudan
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Uneeb Urwat
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Varun Sharma
- Bioinformatics Division, NMC Genetics India Pvt. Ltd., Gurugram, India
| | - Parvaze A Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Asif B Shikari
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Bilal A Bhat
- Mountain Agriculture Research & Extension Station, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Najeebul Rehman Sofi
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, Kansas, USA
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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Badiyal A, Dhiman S, Singh A, Rathour R, Pathania A, Katoch S, Padder BA, Sharma PN. Mapping of adult plant recessive resistance to anthracnose in Indian common bean landrace Baspa/KRC 8. Mol Biol Rep 2024; 51:254. [PMID: 38302755 DOI: 10.1007/s11033-023-09160-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/14/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND The common bean (Phaseolus vulgaris) has become the food of choice owing to its wealthy nutritional profile, leading to a considerable increase in its cultivation worldwide. However, anthracnose has been a major impediment to production and productivity, as elite bean cultivars are vulnerable to this disease. To overcome barriers in crop production, scientists worldwide are working towards enhancing the genetic diversity of crops. One way to achieve this is by introducing novel genes from related crops, including landraces like KRC 8. This particular landrace, found in the North Western Himalayan region, has shown adult plant resistance against anthracnose and also possesses a recessive resistance gene. METHODS AND RESULTS In this study, a population of 179 F2:9 RIL individuals (Jawala × KRC 8) was evaluated at both phenotypic and genotypic levels using over 830 diverse molecular markers to map the resistance gene present in KRC 8. We have successfully mapped a resistance gene to chromosome Pv01 using four SSR markers, namely IAC 238, IAC 235, IAC 259, and BM 146. The marker IAC 238 is closely linked to the gene with a distance of 0.29 cM, while the other markers flank the recessive resistance gene at 10.87 cM (IAC 259), 17.80 cM (BM 146), and 25.22 cM (IAC 235). Previously, a single recessive anthracnose resistance gene (co-8) has been reported in the common bean accession AB 136. However, when we performed PCR amplification with our tightly linked marker IAC 238, we got different amplicons in AB 136 and KRC 8. Interestingly, the susceptible cultivar Jawala produced the same amplicon as AB 136. This observation indicated that the recessive gene present in KRC 8 is different from co-8. As the gene is located far away from the Co-1 locus, we suggest naming the recessive gene co-Indb/co-19. Fine mapping of co-Indb in KRC 8 may provide new insights into the cloning and characterization of this recessive gene so that it can be incorporated into future bean improvement programs. Further, the tightly linked marker IAC 238 can be utilized in marker assisted introgression in future bean breeding programs. CONCLUSION The novel co-Indb gene present in Himalayan landrace KRC 8, showing adult plant resistance against common bean anthracnose, is independent from all the resistance genes previously located on chromosome Pv01.
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Affiliation(s)
- Anila Badiyal
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Shiwali Dhiman
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Amar Singh
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Anju Pathania
- Faculty of Agriculture, DAV University, Jalandhar, 144001, Punjab, India
| | - Shabnam Katoch
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-K Srinagar, Srinagar, 190025, J&K, India.
| | - Prem N Sharma
- Molecular Plant Pathology Laboratory, Department of Plant Pathology, CSK HP Agricultural University, Palampur, 176 062, Himachal Pradesh, India.
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Mohd Shaha FR, Liew PL, Qamaruz Zaman F, Nulit R, Barin J, Rolland J, Yong HY, Boon SH. Genotyping by sequencing for the construction of oil palm ( Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci. PeerJ 2024; 12:e16570. [PMID: 38313025 PMCID: PMC10836210 DOI: 10.7717/peerj.16570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/13/2023] [Indexed: 02/06/2024] Open
Abstract
Background Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis. Methods A mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B). Results A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1-25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS).
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Affiliation(s)
- Fakhrur Razi Mohd Shaha
- ACGT Sdn. Bhd. & Laboratories, Bukit Jalil, Kuala Lumpur, Malaysia
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Pui Ling Liew
- ACGT Sdn. Bhd. & Laboratories, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Faridah Qamaruz Zaman
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Rosimah Nulit
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Jakim Barin
- Wisma Pertanian Sabah, Department of Agriculture Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Justina Rolland
- Wisma Pertanian Sabah, Department of Agriculture Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Hui Yee Yong
- ACGT Sdn. Bhd. & Laboratories, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Soo Heong Boon
- ACGT Sdn. Bhd. & Laboratories, Bukit Jalil, Kuala Lumpur, Malaysia
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Johansen M, Saenko S, Schilthuizen M, Blaxter M, Davison A. Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map. Heredity (Edinb) 2023; 131:327-337. [PMID: 37758900 PMCID: PMC10673960 DOI: 10.1038/s41437-023-00648-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a 'supergene', control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.
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Affiliation(s)
- Margrethe Johansen
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Suzanne Saenko
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Menno Schilthuizen
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angus Davison
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
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Chen X, Wang Y, Guan S, Yan Z, Zhu X, Kuo Y, Wang N, Zhi X, Lian Y, Huang J, Liu P, Li R, Yan L, Qiao J. Application of the PGT-M strategy using single sperm and/or affected embryos as probands for linkage analysis in males with hereditary tumor syndromes without family history. J Hum Genet 2023; 68:813-821. [PMID: 37592134 DOI: 10.1038/s10038-023-01188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023]
Abstract
Hereditary tumor syndromes have garnered substantial attention due to their adverse effects on both the physical and psychological health of patients, as well as the elevated risk of transmission to subsequent generations. This has prompted a growing interest in exploring preimplantation genetic testing (PGT) as a treatment option to mitigate and eliminate these impacts. Several studies have demonstrated that de novo variants have become a great cause of many hereditary tumor syndromes, which introduce certain difficulties to PGT. In the absence of adequate genetic linkage information (parents and offspring), haplotype construction seems unrealizable. In the study, researchers used single sperm or affected embryos as proband to perform single-nucleotide polymorphism linkage analysis for cases with de novo variants. For complicated variants, the strategy that sperm combined with embryo detection will increase accuracy while avoiding the limitations and potential failures of using a single detection material. The study recruited 11 couples with male de novo carriers, including 3 tumor types and 4 genes. To date, 4 couples have been clinically confirmed as pregnant and three healthy babies have been born. The results of amniocentesis or umbilical cord blood verification were consistent with the results of PGT-M. The study aims to introduce the application of the PGT-M strategy in hereditary tumor syndromes.
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Affiliation(s)
- Xi Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Yuqian Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China
| | - Shuo Guan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xiaohui Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ying Kuo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Nan Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xu Zhi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ying Lian
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jin Huang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, China.
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China.
- Beijing Advanced Innovation Center for Genomics, Beijing, 100191, China.
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Eiberg H, Olsson JB, Bak M, Bang-Berthelsen CH, Troelsen JT, Hansen L. A family with ulcerative colitis maps to 7p21.1 and comprises a region with regulatory activity for the aryl hydrocarbon receptor gene. Eur J Hum Genet 2023; 31:1440-1446. [PMID: 36732664 PMCID: PMC10689720 DOI: 10.1038/s41431-023-01298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/16/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
We have mapped a locus on chromosome 7p22.3-7p15.3 spanning a 22.4 Mb region for ulcerative colitis (UC) by whole genome linkage analyses of a large Danish family. The family represent three generations with UC segregating as an autosomal dominant trait with variable expressivity. The whole-genome scan resulted in a logarithm of odds score (LOD score) of Z = 3.31, and a whole genome sequencing (WGS) of two affected excluded disease-causing mutations in the protein coding genes. Two rare heterozygote variants, rs182281985:G>A and rs541426369:G>A, both with low allele frequencies (MAF A:0.0001, gnomAD ver3.1.2), were found in clusters of ChiP-seq transcription factors binding sites close to the AHR (aryl hydrocarbon receptor) gene and the UC associated SNP rs1077773:G>A. Testing the two SNPs in a promoter reporter assay for regulatory activity revealed that rs182281985:G>A influenced the AHR promoter. These results suggest a regulatory region that include rs182281985:G>A close to the UC GWAS SNP rs1077773:G>A and further demonstrate evidence that the AHR gene on the 7p-tel region is a candidate susceptible gene for UC.
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Affiliation(s)
- Hans Eiberg
- RCLINK, Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark.
| | - Josephine B Olsson
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Naestved, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Claus Heiner Bang-Berthelsen
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kemitorvet building 202, 2800 Kgs, Lyngby, Denmark
| | - Jesper T Troelsen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Lars Hansen
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200, Copenhagen N, Denmark
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12
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Ellis N, Hofer J, Sizer-Coverdale E, Lloyd D, Aubert G, Kreplak J, Burstin J, Cheema J, Bal M, Chen Y, Deng S, Wouters RHM, Steuernagel B, Chayut N, Domoney C. Recombinant inbred lines derived from wide crosses in Pisum. Sci Rep 2023; 13:20408. [PMID: 37990072 PMCID: PMC10663473 DOI: 10.1038/s41598-023-47329-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023] Open
Abstract
Genomic resources are becoming available for Pisum but to link these to phenotypic diversity requires well marked populations segregating for relevant traits. Here we describe two such resources. Two recombinant inbred populations, derived from wide crosses in Pisum are described. One high resolution mapping population involves cv Caméor, for which the first pea whole genome assembly was obtained, crossed to JI0281, a basally divergent P. sativum sativum landrace from Ethiopia. The other is an inter sub-specific cross between P. s. sativum and the independently domesticated P. s. abyssinicum. The corresponding genetic maps provide information on chromosome level sequence assemblies and identify structural differences between the genomes of these two Pisum subspecies. In order to visualise chromosomal translocations that distinguish the mapping parents, we created a simplified version of Threadmapper to optimise it for interactive 3-dimensional display of multiple linkage groups. The genetic mapping of traits affecting seed coat roughness and colour, plant height, axil ring pigmentation, leaflet number and leaflet indentation enabled the definition of their corresponding genomic regions. The consequence of structural rearrangement for trait analysis is illustrated by leaf serration. These analyses pave the way for identification of the underlying genes and illustrate the utility of these publicly available resources. Segregating inbred populations derived from wide crosses in Pisum, together with the associated marker data, are made publicly available for trait dissection. Genetic analysis of these populations is informative about chromosome scale assemblies, structural diversity in the pea genome and has been useful for the fine mapping of several discrete and quantitative traits.
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Affiliation(s)
- N Ellis
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK.
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK.
| | - J Hofer
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - E Sizer-Coverdale
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
- Germinal Horizon, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - D Lloyd
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
- Germinal Horizon, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, SY23 3EB, UK
| | - G Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - J Cheema
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - M Bal
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Y Chen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - S Deng
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - R H M Wouters
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - B Steuernagel
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - N Chayut
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - C Domoney
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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Xu YF, Ma FF, Zhang JP, Liu H, Li LH, An DG. Unraveling the genetic basis of grain number-related traits in a wheat-Agropyron cristatum introgressed line through high-resolution linkage mapping. BMC Plant Biol 2023; 23:563. [PMID: 37964231 PMCID: PMC10647127 DOI: 10.1186/s12870-023-04547-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/19/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND Grain number per spike (GNS) is a pivotal determinant of grain yield in wheat. Pubing 3228 (PB3228), a wheat-Agropyron cristatum germplasm, exhibits a notably higher GNS. RESULTS In this study, we developed a recombinant inbred line (RIL) population derived from PB3228/Gao8901 (PG-RIL) and constructed a high-density genetic map comprising 101,136 loci, spanning 4357.3 cM using the Wheat 660 K SNP array. The genetic map demonstrated high collinearity with the wheat assembly IWGSC RefSeq v1.0. Traits related to grain number and spikelet number per spike were evaluated in seven environments for quantitative trait locus (QTL) analysis. Five environmentally stable QTLs were detected in at least three environments. Among these, two major QTLs, QGns-4A.2 and QGns-1A.1, associated with GNS, exhibited positive alleles contributed by PB3228. Further, the conditional QTL analysis revealed a predominant contribution of PB3228 to the GNS QTLs, with both grain number per spikelet (GNSL) and spikelet number per spike (SNS) contributing to the overall GNS trait. Four kompetitive allele-specific PCR (KASP) markers that linked to QGns-4A.2 and QGns-1A.1 were developed and found to be effective in verifying the QTL effect within a diversity panel. Compared to previous studies, QGns-4A.2 exhibited stability across different trials, while QGns-1A.1 represents a novel QTL. The results from unconditional and conditional QTL analyses are valuable for dissecting the genetic contribution of the component traits to GNS at the individual QTL level and for understanding the genetic basis of the superior grain number character in PB3228. The KASP markers can be utilized in marker-assisted selection for enhancing GNS. CONCLUSIONS Five environmentally stable QTLs related to grain number and spikelet number per spike were identified. PB3228 contributed to the majority of the QTLs associated with GNS.
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Affiliation(s)
- Yun-Feng Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Fei-Fei Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Jin-Peng Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Li-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Diao-Guo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China.
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Lovatto M, Gonçalves-Vidigal MC, Vaz Bisneta M, Calvi AC, Mazucheli J, Vidigal Filho PS, Miranda EGR, Melotto M. Responsiveness of Candidate Genes on CoPv01CDRK/PhgPv01CDRK Loci in Common Bean Challenged by Anthracnose and Angular Leaf Spot Pathogens. Int J Mol Sci 2023; 24:16023. [PMID: 38003212 PMCID: PMC10671028 DOI: 10.3390/ijms242216023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 11/26/2023] Open
Abstract
Anthracnose (ANT) and angular leaf spot (ALS) are significant diseases in common bean, leading to considerable yield losses under specific environmental conditions. The California Dark Red Kidney (CDRK) bean cultivar is known for its resistance to multiple races of both pathogens. Previous studies have identified the CoPv01CDRK/PhgPv01CDRK resistance loci on chromosome Pv01. Here, we evaluated the expression levels of ten candidate genes near the CoPv01CDRK/PhgPv01CDRK loci and plant defense genes using quantitative real-time PCR in CDRK cultivar inoculated with races 73 of Colletotrichum lindemuthianum and 63-39 of Pseudocercospora griseola. Gene expression analysis revealed that the Phvul.001G246300 gene exhibited the most elevated levels, showing remarkable 7.8-fold and 8.5-fold increases for ANT and ALS, respectively. The Phvul.001G246300 gene encodes an abscisic acid (ABA) receptor with pyrabactin resistance, PYR1-like (PYL) protein, which plays a central role in the crosstalk between ABA and jasmonic acid responses. Interestingly, our results also showed that the other defense genes were initially activated. These findings provide critical insights into the molecular mechanisms underlying plant defense against these diseases and could contribute to the development of more effective disease management strategies in the future.
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Affiliation(s)
- Maike Lovatto
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | | | - Mariana Vaz Bisneta
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | - Alexandre Catto Calvi
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | - Josmar Mazucheli
- Departamento de Estatística, Universidade Estadual de Maringá, Maringá 87020-900, Brazil
| | | | | | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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15
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Roshani M, Taheri M, Goodarzi A, Yosefimashouf R, Shokoohizadeh L. Evaluation of antibiotic resistance, toxin-antitoxin systems, virulence factors, biofilm-forming strength and genetic linkage of Escherichia coli strains isolated from bloodstream infections of leukemia patients. BMC Microbiol 2023; 23:327. [PMID: 37925405 PMCID: PMC10625236 DOI: 10.1186/s12866-023-03081-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/22/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND One of the most common complications in patients with febrile neutropenia, lymphoma, leukemia, and multiple myeloma is a bloodstream infection (BSI). OBJECTIVE This study aimed to evaluate the antibiotic resistance patterns, virulence factors, biofilm-forming strength, and genetic linkage of Escherichia coli strains isolated from bloodstream infections (BSIs) of leukemia patients. METHODS The study conducted in Iran from June 2021 to December 2022, isolated 67 E. coli strains from leukemia patients' bloodstream infections in hospitals in two different areas. Several techniques including disk diffusion and broth microdilution were used to identify patterns of antibiotic resistance, microtiter plate assay to measure biofilm formation, and PCR to evaluate the prevalence of different genes such as virulence factors, toxin-antitoxin systems, resistance to β-lactams and fluoroquinolone antibiotics of E. coli strains. Additionally, the genetic linkage of the isolates was analyzed using the Enterobacterial Repeat Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) method. RESULTS The results showed that higher frequency of BSI caused by E. coli in man than female patients, and patients with acute leukemia had a higher frequency of BSI. Ampicillin and Amoxicillin-clavulanic acid showed the highest resistance, while Imipenem was identified as a suitable antibiotic for treating BSIs by E. coli. Multidrug-resistant (MDR) phenotypes were present in 22% of the isolates, while 53% of the isolates were ESBL-producing with the blaCTX-M gene as the most frequent β-lactamase gene. The fluoroquinolone resistance genes qnrB and qnrS were present in 50% and 28% of the isolates, respectively. More than 80% of the isolates showed the ability to form biofilms. The traT gene was more frequent than other virulence genes. The toxin-antitoxin system genes (mazF, ccdAB, and relB) showed a comparable frequency. The genetic diversity was detected in E. coli isolates. CONCLUSION Our results demonstrate that highly diverse, resistant and pathogenic E. coli clones are circulating among leukemia patients in Iranian hospitals. More attention should be paid to the treatment and management of E. coli bloodstream infections in patients with leukemia.
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Affiliation(s)
- Mahdaneh Roshani
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Taheri
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Alireza Goodarzi
- Infectious Disease Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rassoul Yosefimashouf
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Leili Shokoohizadeh
- Department of Medical Laboratory Sciences, School of Paramedicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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Oh JE, Kim JE, Kim J, Lee MH, Lee K, Kim TH, Jo SH, Lee JH. Development of an SNP marker set for marker-assisted backcrossing using genotyping-by-sequencing in tetraploid perilla. Mol Genet Genomics 2023; 298:1435-1447. [PMID: 37725237 DOI: 10.1007/s00438-023-02066-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/26/2023] [Indexed: 09/21/2023]
Abstract
High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2326 and 2454 SNP markers that spanned a total genetic distance of 2133 cM across 16 linkage groups and 2169 cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.
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Affiliation(s)
- Jae-Eun Oh
- SEEDERS Inc, Daejeon, 34912, Republic of Korea
- Department of Bio-AI Convergence, Chungnam National University, Daejeon, Republic of Korea
| | - Ji-Eun Kim
- SEEDERS Inc, Daejeon, 34912, Republic of Korea
| | - Jangmi Kim
- SEEDERS Inc, Daejeon, 34912, Republic of Korea
| | - Myoung-Hee Lee
- National Institute of Crop Science, RDA, Miryang, 50424, Republic of Korea
| | - Keunpyo Lee
- National Academy of Agricultural Science, RDA, Wanju, 55365, Republic of Korea
| | - Tae-Ho Kim
- National Academy of Agricultural Science, RDA, Wanju, 55365, Republic of Korea
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Feng J, Yao F, Wang M, See DR, Chen X. Molecular Mapping of Yr85 and Comparison with Other Genes for Resistance to Stripe Rust on Wheat Chromosome 1B. Plant Dis 2023; 107:3585-3591. [PMID: 37221244 DOI: 10.1094/pdis-11-22-2600-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most serious plant diseases worldwide. Resistant cultivars are the most effective way to control the disease. YrTr1 is an important stripe rust resistance gene that has been used in wheat breeding programs and is represented in the host differential set to identify P. striiformis f. sp. tritici races in the United States. To map YrTr1, AvSYrTr1NIL was backcrossed to its recurrent parent Avocet S (AvS). Seedlings of BC7F2, BC7F3, and BC8F1 populations were tested with YrTr1-avirulent races under controlled conditions, and BC7F2 plants were genotyped using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. YrTr1 was mapped to the short arm of chromosome 1B using four SSR and seven SNP markers. The genetic distances of YrTr1 from the nearest flanking markers IWA2583 and IWA7480 were 1.8 and 1.3 centimorgans (cM), respectively. DNA amplification of a set of 21 Chinese Spring (CS) nulli-tetrasomic lines and seven CS 1B deletion lines with three SSR markers confirmed the chromosome arm location and further placed the gene in chromosomal bin region 1BS18 (0.5). The gene was determined to be about 7.4 cM proximal to Yr10. Based on multirace response array and chromosomal location, YrTr1 was determined to be different from other permanently named stripe rust resistance genes in chromosome arm 1BS and was named Yr85.
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Affiliation(s)
- Junyan Feng
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Fangjie Yao
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- Key Laboratory of Wheat Biology and Genetic Improvement in Southwestern China, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610061, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Deven R See
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
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Che Y, Yang Y, Yang Y, Wei L, Guo J, Yang X, Li X, Liu W, Li L. Construction of a high-density genetic map and mapping of a spike length locus for rye. PLoS One 2023; 18:e0293604. [PMID: 37903124 PMCID: PMC10615298 DOI: 10.1371/journal.pone.0293604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
Genetic maps provide the foundation for QTL mapping of important traits of crops. As a valuable food and forage crop, rye (Secale cereale L., RR) is also one of the tertiary gene sources of wheat, especially wild rye, Secale cereale subsp. segetale, possessing remarkable stress tolerance, tillering capacity and numerous valuable traits. In this study, based on the technique of specific-locus amplified fragment sequencing (SLAF-seq), a high-density single nucleotide polymorphism (SNP) linkage map of the cross-pollinated (CP) hybrid population crossed by S. cereale L (female parent) and S. cereale subsp. segetale (male parent) was successfully constructed. Following preprocessing, the number of 1035.11 M reads were collected and 2425800 SNP were obtained, of which 409134 SNP were polymorphic. According to the screening process, 9811 SNP markers suitable for constructing linkage groups (LGs) were selected. Subsequently, all of the markers with MLOD values lower than 3 were filtered out. Finally, an integrated map was constructed with 4443 markers, including 1931 female mapping markers and 3006 male mapping markers. A major quantitative trait locus (QTL) linked with spike length (SL) was discovered at 73.882 cM on LG4, which explained 25.29% of phenotypic variation. Meanwhile two candidate genes for SL, ScWN4R01G329300 and ScWN4R01G329600, were detected. This research presents the first high-quality genetic map of rye, providing a substantial number of SNP marker loci that can be applied to marker-assisted breeding. Additionally, the finding could help to use SLAF marker mapping to identify certain QTL contributing to important agronomic traits. The QTL and the candidate genes identified through the high-density genetic map above may provide diverse potential gene resources for the genetic improvement of rye.
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Affiliation(s)
- Yonghe Che
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yunjie Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yanping Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Lai Wei
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Juan Guo
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Yang T, Amanullah S, Li S, Cheng R, Zhang C, Zhao Z, Liu H, Luan F, Wang X. Molecular Mapping of Putative Genomic Regions Controlling Fruit and Seed Morphology of Watermelon. Int J Mol Sci 2023; 24:15755. [PMID: 37958737 PMCID: PMC10650541 DOI: 10.3390/ijms242115755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
The genetic regulatory basis of qualitative and quantitative phenotypes of watermelon is being investigated in different types of molecular and genetic breeding studies around the world. In this study, biparental F2 mapping populations were developed over two experimental years, and the collected datasets of fruit and seed traits exhibited highly significant correlations. Whole-genome resequencing of comparative parental lines was performed and detected single nucleotide polymorphism (SNP) loci were converted into cleaved amplified polymorphic sequence (CAPS) markers. The screened polymorphic markers were genotyped in segregating populations and two genetic linkage maps were constructed, which covered a total of 2834.28 and 2721.45 centimorgan (cM) genetic lengths, respectively. A total of 22 quantitative trait loci (QTLs) for seven phenotypic traits were mapped; among them, five stable and major-effect QTLs (PC-8-1, SL-9-1, SWi-9-1, SSi-9-1, and SW-6-1) and four minor-effect QTLs (PC-2-1 and PC-2-2; PT-2-1 and PT-2-2; SL-6-1 and SSi-6-2; and SWi-6-1 and SWi-6-2) were observed with 3.77-38.98% PVE. The adjacent QTL markers showed a good fit marker-trait association, and a significant allele-specific contribution was also noticed for genetic inheritance of traits. Further, a total of four candidate genes (Cla97C09G179150, Cla97C09G179350, Cla97C09G180040, and Cla97C09G180100) were spotted in the stable colocalized QTLs of seed size linked traits (SL-9-1 and SWi-9-1) that showed non-synonymous type mutations. The gene expression trends indicated that the seed morphology had been formed in the early developmental stage and showed the genetic regulation of seed shape formation. Hence, we think that our identified QTLs and genes would provide powerful genetic insights for marker-assisted breeding aimed at improving the quality traits of watermelon.
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Affiliation(s)
- Tiantian Yang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Sikandar Amanullah
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Shenglong Li
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Rui Cheng
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Chen Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Zhengxiang Zhao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Hongyu Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
| | - Xuezheng Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (T.Y.); (S.L.); (R.C.); (Z.Z.); (H.L.); (F.L.)
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin 150030, China
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20
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Zhang Y, Li J, Chu P, Shang R, Yin S, Wang T. Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus. BMC Genomics 2023; 24:645. [PMID: 37891474 PMCID: PMC10604518 DOI: 10.1186/s12864-023-09740-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Takifugu fasciatus is an aquaculture species with high economic value. In recent years, problems such as environmental pollution and inbreeding have caused a serious decline in T. fasciatus germplasm resources. In this study, a high-density genetic linkage map was constructed by whole-genome resequencing. The map consists of 4891 bin markers distributed across 22 linkage groups (LGs), with a total genetic coverage of 2381.353 cM and a mean density of 0.535 cM. Quantitative trait locus (QTL) localization analysis showed that a total of 19 QTLs associated with growth traits of T. fasciatus in the genome-wide significance threshold range, distributed on 11 LGs. In addition, 11 QTLs associated with cold tolerance traits were identified, each scattered on a different LG. Furthermore, we used QTL localization analysis to screen out three candidate genes (IGF1, IGF2, ADGRB) related to growth in T. fasciatus. Meanwhile, we screened three candidate genes (HSP90, HSP70, and HMGB1) related to T. fasciatus cold tolerance. Our study can provide a theoretical basis for the selection and breeding of cold-tolerant or fast-growing T. fasciatus.
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Affiliation(s)
- Ying Zhang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Jie Li
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Peng Chu
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Ruhua Shang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Shaowu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Tao Wang
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
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Feng Y, Yang C, Zhang J, Qiao J, Wang B, Zhao Y. Construction of a High-Density Paulownia Genetic Map and QTL Mapping of Important Phenotypic Traits Based on Genome Assembly and Whole-Genome Resequencing. Int J Mol Sci 2023; 24:15647. [PMID: 37958630 PMCID: PMC10647314 DOI: 10.3390/ijms242115647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative trait locus (QTL) mapping based on a genetic map is a very effective method of marker-assisted selection in breeding, and whole-genome resequencing is one of the useful methods to obtain high-density genetic maps. In this study, the hybrid assembly of Illumina, PacBio, and chromatin interaction mapping data was used to construct high-quality chromosomal genome sequences of Paulownia fortunei, with a size of 476.82 Mb, a heterozygosity of 0.52%, and a contig and scaffold N50s of 7.81 Mb and 21.81 Mb, respectively. Twenty scaffolds with a total length of 437.72 Mb were assembled into 20 pseudochromosomes. Repeat sequences with a total length of 243.96 Mb accounted for 51.16% of the entire genome. In all, 26,903 protein-coding gene loci were identified, and 26,008 (96.67%) genes had conserved functional motifs. Further comparative genomics analysis preliminarily showed that the split of P. fortunei with Tectona grandis likely occurred 38.8 (33.3-45.1) million years ago. Whole-genome resequencing was used to construct a merged genetic map of 20 linkage groups, with 2993 bin markers (3,312,780 SNPs), a total length of 1675.14 cm, and an average marker interval of 0.56 cm. In total, 73 QTLs for important phenotypic traits were identified (19 major QTLs with phenotypic variation explained ≥ 10%), including 10 for the diameter at breast height, 7 for the main trunk height, and 56 for branch-related traits. These results not only enrich P. fortunei genomic data but also form a solid foundation for fine QTL mapping and key marker/gene mining of Paulownia, which is of great significance for the directed genetic improvement of these species.
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Affiliation(s)
- Yanzhi Feng
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Chaowei Yang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Jiajia Zhang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Jie Qiao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Baoping Wang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Yang Zhao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
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Yadava YK, Chaudhary P, Yadav S, Rizvi AH, Kumar T, Srivastava R, Soren KR, Bharadwaj C, Srinivasan R, Singh NK, Jain PK. Genetic mapping of quantitative trait loci associated with drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 2023; 13:17623. [PMID: 37848483 PMCID: PMC10582051 DOI: 10.1038/s41598-023-44990-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Elucidation of the genetic basis of drought tolerance is vital for genomics-assisted breeding of drought tolerant crop varieties. Here, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphisms (SNPs) in recombinant inbred lines (RILs) derived from a cross between a drought tolerant chickpea variety, Pusa 362 and a drought sensitive variety, SBD 377. The GBS identified a total of 35,502 SNPs and subsequent filtering of these resulted in 3237 high-quality SNPs included in the eight linkage groups. Fifty-one percent of these SNPs were located in the genic regions distributed throughout the genome. The high density linkage map has total map length of 1069 cm with an average marker interval of 0.33 cm. The linkage map was used to identify 9 robust and consistent QTLs for four drought related traits viz. membrane stability index, relative water content, seed weight and yield under drought, with percent variance explained within the range of 6.29%-90.68% and LOD scores of 2.64 to 6.38, which were located on five of the eight linkage groups. A genomic region on LG 7 harbors quantitative trait loci (QTLs) explaining > 90% phenotypic variance for membrane stability index, and > 10% PVE for yield. This study also provides the first report of major QTLs for physiological traits such as membrane stability index and relative water content for drought stress in chickpea. A total of 369 putative candidate genes were identified in the 6.6 Mb genomic region spanning these QTLs. In-silico expression profiling based on the available transcriptome data revealed that 326 of these genes were differentially expressed under drought stress. KEGG analysis resulted in reduction of candidate genes from 369 to 99, revealing enrichment in various signaling pathways. Haplotype analysis confirmed 5 QTLs among the initially identified 9 QTLs. Two QTLs, qRWC1.1 and qYLD7.1, were chosen based on high SNP density. Candidate gene-based analysis revealed distinct haplotypes in qYLD7.1 associated with significant phenotypic differences, potentially linked to pathways for secondary metabolite biosynthesis. These identified candidate genes bolster defenses through flavonoids and phenylalanine-derived compounds, aiding UV protection, pathogen resistance, and plant structure.The study provides novel genomic regions and candidate genes which can be utilized in genomics-assisted breeding of superior drought tolerant chickpea cultivars.
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Affiliation(s)
- Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Pooja Chaudhary
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - Aqeel Hasan Rizvi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Tapan Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rachna Srivastava
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - K R Soren
- ICAR-Indian Institute of Pulses Research, Kanpur, 208024, India
| | - C Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - R Srinivasan
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, IARI Campus, New Delhi, 110012, India.
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23
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Favre F, Jourda C, Grisoni M, Chiroleu F, Dijoux JB, Jade K, Rivallan R, Besse P, Charron C. First Vanilla planifolia High-Density Genetic Linkage Map Provides Quantitative Trait Loci for Resistance to Fusarium oxysporum. Plant Dis 2023; 107:2997-3006. [PMID: 36856646 DOI: 10.1094/pdis-10-22-2386-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium oxysporum f. sp. radicis-vanillae (Forv), the causal agent of root and stem rot disease, is the main pathogen affecting vanilla production. Sources of resistance have been reported in Vanilla planifolia G. Jackson ex Andrews, the main cultivated vanilla species. In this study, we developed the first high-density genetic map in this species with 1,804 genotyping-by-sequencing (GBS)-generated single nucleotide polymorphism (SNP) markers using 125 selfed progenies of the CR0040 traditional vanilla cultivar. Sixteen linkage groups (LG) were successfully constructed, with a mean of 113 SNPs and an average length of 207 cM per LG. The map had a high density with an average of 5.45 SNP every 10 cM and an average distance of 1.85 cM between adjacent markers. The first three LG were aligned against the first assembled chromosome of CR0040, and the other 13 LG were correctly associated with the other 13 assembled chromosomes. The population was challenged with the highly pathogenic Forv strain Fo072 using the root-dip inoculation method. Five traits were mapped, and 20 QTLs were associated with resistance to Fo072. Among the genes retrieved in the CR0040 physical regions associated with QTLs, genes potentially involved in biotic resistance mechanisms, coding for kinases, E3 ubiquitin ligases, pentatricopeptide repeat-containing proteins, and one leucine-rich repeat receptor underlying the qFo72_08.1 QTL have been highlighted. This study should provide useful resources for marker-assisted selection in V. planifolia.
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Affiliation(s)
- Félicien Favre
- University of Reunion Island, UMR PVBMT, F-97410 St. Pierre, Reunion Island, France
| | - Cyril Jourda
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| | | | | | | | - Katia Jade
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pascale Besse
- University of Reunion Island, UMR PVBMT, F-97410 St. Pierre, Reunion Island, France
| | - Carine Charron
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
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Zhang R, Wu H, Li Y, Huang Z, Yin Z, Yang CX, Du ZQ. GWLD: an R package for genome-wide linkage disequilibrium analysis. G3 (Bethesda) 2023; 13:jkad154. [PMID: 37431944 PMCID: PMC10468308 DOI: 10.1093/g3journal/jkad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/14/2023] [Accepted: 06/26/2023] [Indexed: 07/12/2023]
Abstract
Linkage disequilibrium (LD) analysis is fundamental to the investigation of the genetic architecture of complex traits (e.g. human disease, animal and plant breeding) and population structure and evolution dynamics. However, until now, studies primarily focus on LD status between genetic variants located on the same chromosome. Moreover, genome (re)sequencing produces unprecedented numbers of genetic variants, and fast LD computation becomes a challenge. Here, we have developed GWLD, a parallelized and generalized tool designed for the rapid genome-wide calculation of LD values, including conventional D/D', r2, and (reduced) mutual information (MI and RMI) measures. LD between genetic variants within and across chromosomes can be rapidly computed and visualized in either an R package or a standalone C++ software package. To evaluate the accuracy and speed of LD calculation, we conducted comparisons using 4 real datasets. Interchromosomal LD patterns observed potentially reflect levels of selection intensity across different species. Both versions of GWLD, the R package (https://github.com/Rong-Zh/GWLD/GWLD-R) and the standalone C++ software (https://github.com/Rong-Zh/GWLD/GWLD-C++), are freely available on GitHub.
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Affiliation(s)
- Rong Zhang
- College of Animal Science, Yangtze University, Jingzhou 434025, Hubei, China
| | - Huaxuan Wu
- College of Animal Science, Yangtze University, Jingzhou 434025, Hubei, China
| | - Yasai Li
- College of Animal Science, Yangtze University, Jingzhou 434025, Hubei, China
| | - Zehang Huang
- College of Animal Science, Yangtze University, Jingzhou 434025, Hubei, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou 434025, Hubei, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou 434025, Hubei, China
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Shen X, Niu YC, Uichanco JAV, Phua N, Bhandare P, Thevasagayam NM, Prakki SRS, Orbán L. Mapping of a major QTL for increased robustness and detection of genome assembly errors in Asian seabass (Lates calcarifer). BMC Genomics 2023; 24:449. [PMID: 37558985 PMCID: PMC10413685 DOI: 10.1186/s12864-023-09513-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND For Asian seabass (Lates calcarifer, Bloch 1790) cultured at sea cages various aquatic pathogens, complex environmental and stress factors are considered as leading causes of disease, causing tens of millions of dollars of annual economic losses. Over the years, we conducted farm-based challenges by exposing Asian seabass juveniles to complex natural environmental conditions. In one of these challenges, we collected a total of 1,250 fish classified as either 'sensitive' or 'robust' individuals during the 28-day observation period. RESULTS We constructed a high-resolution linkage map with 3,089 SNPs for Asian seabass using the double digest Restriction-site Associated DNA (ddRAD) technology and a performed a search for Quantitative Trait Loci (QTL) associated with robustness. The search detected a major genome-wide significant QTL for increased robustness in pathogen-infected marine environment on linkage group 11 (ASB_LG11; 88.9 cM to 93.6 cM) with phenotypic variation explained of 81.0%. The QTL was positioned within a > 800 kb genomic region located at the tip of chromosome ASB_LG11 with two Single Nucleotide Polymorphism markers, R1-38468 and R1-61252, located near to the two ends of the QTL. When the R1-61252 marker was validated experimentally in a different mass cross population, it showed a statistically significant association with increased robustness. The majority of thirty-six potential candidate genes located within the QTL have known functions related to innate immunity, stress response or disease. By utilizing this ddRAD-based map, we detected five mis-assemblies corresponding to four chromosomes, namely ASB_LG8, ASB_LG9, ASB_LG15 and ASB_LG20, in the current Asian seabass reference genome assembly. CONCLUSION According to our knowledge, the QTL associated with increased robustness is the first such finding from a tropical fish species. Depending on further validation in other stocks and populations, it might be potentially useful for selecting robust Asian seabass lines in selection programs.
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Affiliation(s)
- Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.
- Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore.
| | | | - Joseph Angelo V Uichanco
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- James Cook University Singapore, Singapore, Singapore
| | - Norman Phua
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Present Address: School of Chemical & Life Sciences, Life Sciences Applied Research Group, Nanyang Polytechnic, Singapore, Singapore
| | - Pranjali Bhandare
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Present address: Theodor Boven Institute (Biocenter), University of Würzburg, Würzburg, Germany
| | - Natascha May Thevasagayam
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Present address: Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sai Rama Sridatta Prakki
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Present address: Infectious Disease Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore.
- Frontline Fish Genomics Research Group, Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Georgikon Campus, Hungarian University of Agriculture and Life Sciences, Keszthely, Hungary.
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Biswas S, Nain M, Ahmad SS, Sharma A. Role of Human Twin Studies to Identify Genetic Linkage of Malaria Pathogenesis and Outcomes. Am J Trop Med Hyg 2023; 109:241-247. [PMID: 37277110 PMCID: PMC10397443 DOI: 10.4269/ajtmh.23-0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/01/2023] [Indexed: 06/07/2023] Open
Abstract
Malaria remains a major public health challenge that needs attention, especially when the world is aiming at malaria elimination in the near future. It is crucial to understand the underlying genetic factors and epigenetics involved in malaria susceptibility and the dynamics of host immune responses that affect disease outcomes and relapses in Plasmodium vivax and Plasmodium ovale. Studies in newborn and adult twins can help in understanding the comparative roles of environmental and genetic factors on disease pathogenesis and outcome. These studies can help in providing insights into the factors responsible for malaria susceptibility, clinical presentation, responsiveness toward existing as well as candidate antimalarials, and even identification of novel therapeutic targets. The results and outcomes from twin studies can be further applied to the entire population. In the present manuscript, we analyze the available literature on malaria and human twins and discuss the significance and benefits of twin studies to help in better understanding malaria.
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Affiliation(s)
- Shibani Biswas
- ICMR-National Institute of Malaria Research, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Minu Nain
- ICMR-National Institute of Malaria Research, New Delhi, India
| | | | - Amit Sharma
- Academy of Scientific and Innovative Research, Ghaziabad, India
- Molecular Medicine, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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Shrestha SL, Tobias CM, Bhandari HS, Bragg J, Nayak S, Goddard K, Allen F. Mapping quantitative trait loci for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) multiple populations. G3 (Bethesda) 2023; 13:jkad061. [PMID: 36947434 PMCID: PMC10151402 DOI: 10.1093/g3journal/jkad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/15/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
Switchgrass can be used as an alternative source for bioenergy production. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Quantitative trait loci (QTL) mapping can help to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped 7 hybrid populations and one combined of 2 hybrid populations (30-96 F1s) derived from Alamo and Kanlow genotypes. The populations were evaluated for biomass yield, plant height, and crown size in a simulated-sward plot with 2 replications at 2 locations in Tennessee from 2019 to 2021. The populations showed significant genetic variation for the evaluated traits and exhibited transgressive segregation. The 17,251 single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS) were used to construct a linkage map using a fast algorithm for multiple outbred families. The linkage map spanned 1,941 cM with an average interval of 0.11 cM between SNPs. The QTL analysis was performed on evaluated traits for each and across environments (year and location) that identified 5 QTL for biomass yield (logarithm of the odds, LOD 3.12-4.34), 4 QTL for plant height (LOD 3.01-5.64), and 7 QTL for crown size (LOD 3.0-4.46) (P ≤ 0.05). The major QTL for biomass yield, plant height, and crown size resided on chromosomes 8N, 6N, and 8K explained phenotypic variations of 5.6, 5.1, and 6.6%, respectively. SNPs linked to QTL could be incorporated into marker-assisted breeding to maximize the selection gain in switchgrass breeding.
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Affiliation(s)
- Surya L Shrestha
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Christian M Tobias
- United States Department of Agriculture (USDA) Agricultural Research Service (ARS), Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Plant Systems-Production, USDA National Institute of Food and Agriculture (NIFA), Beacon Complex, USA
| | - Hem S Bhandari
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Jennifer Bragg
- United States Department of Agriculture (USDA) Agricultural Research Service (ARS), Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
| | - Santosh Nayak
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
- USDA ARS, Crop Improvement and Protection Research Unit, 1636 E Alisal Street, Salinas, CA 93905, USA
| | - Ken Goddard
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Fred Allen
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
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Zajac GJM, Gagliano Taliun SA, Sidore C, Graham SE, Åsvold BO, Brumpton B, Nielsen JB, Zhou W, Gabrielsen M, Skogholt AH, Fritsche LG, Schlessinger D, Cucca F, Hveem K, Willer CJ, Abecasis GR. A fast linkage method for population GWAS cohorts with related individuals. Genet Epidemiol 2023; 47:231-248. [PMID: 36739617 PMCID: PMC10027464 DOI: 10.1002/gepi.22516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 02/07/2023]
Abstract
Linkage analysis, a class of methods for detecting co-segregation of genomic segments and traits in families, was used to map disease-causing genes for decades before genotyping arrays and dense SNP genotyping enabled genome-wide association studies in population samples. Population samples often contain related individuals, but the segregation of alleles within families is rarely used because traditional linkage methods are computationally inefficient for larger datasets. Here, we describe Population Linkage, a novel application of Haseman-Elston regression as a method of moments estimator of variance components and their standard errors. We achieve additional computational efficiency by using modern methods for detection of IBD segments and variance component estimation, efficient preprocessing of input data, and minimizing redundant numerical calculations. We also refined variance component models to account for the biases in population-scale methods for IBD segment detection. We ran Population Linkage on four blood lipid traits in over 70,000 individuals from the HUNT and SardiNIA studies, successfully detecting 25 known genetic signals. One notable linkage signal that appeared in both was for low-density lipoprotein (LDL) cholesterol levels in the region near the gene APOE (LOD = 29.3, variance explained = 4.1%). This is the region where the missense variants rs7412 and rs429358, which together make up the ε2, ε3, and ε4 alleles each account for 2.4% and 0.8% of variation in circulating LDL cholesterol. Our results show the potential for linkage analysis and other large-scale applications of method of moments variance components estimation.
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Affiliation(s)
- Gregory J M Zajac
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Sarah A Gagliano Taliun
- Department of Medicine and Department of Neurosciences, Université de Montréal, Montréal, Québec, Canada
- Montréal Heart Institute, Montréal, Québec, Canada
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Sarah E Graham
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Bjørn O Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Ben Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jonas B Nielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Maiken Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne H Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars G Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | | | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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Amin M, Gragnoli C. Genome-wide linkage and association study identifies novel genes and pathways implicated in polycystic ovarian syndrome. Eur Rev Med Pharmacol Sci 2023; 27:3719-3732. [PMID: 37140321 DOI: 10.26355/eurrev_202304_32171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
OBJECTIVE Polycystic ovarian syndrome (PCOS) is a complex heterogeneous condition that affects women of reproductive age, conferring increased cardiovascular morbidity and mortality. The syndrome is characterized by oligomenorrhea, hyperandrogenism, and/or polycystic ovaries and is often associated with obesity and type 2 diabetes. Individuals are predisposed to PCOS by environmental factors and risk variants in genes mostly involved in ovarian steroidogenesis and/or insulin resistance. Genetic risk factors have been identified by both familial and genome-wide (GW) association studies. However, most genetic components are still unknown and missing heritability needs to be elucidated. To learn more about the genetic determinants of PCOS, we performed a GW study in genetically highly homogeneous peninsular families. PATIENTS AND METHODS We conducted the first GW-linkage and linkage disequilibrium (i.e., linkage + association) study in Italian families with PCOS. RESULTS We identified several novel risk variants, genes, and pathways potentially implicated in the pathogenesis of PCOS. Specifically, we detected 79 novel variants with significant GW-linkage and/or -association with PCOS across 4 inheritance models (p < 0.00005), of which 50 variants were within 45 novel PCOS-risk genes. CONCLUSIONS This is the first GW-linkage and linkage disequilibrium study performed in peninsular Italian families and reporting novel genes in PCOS.
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Affiliation(s)
- M Amin
- INSERM, US14-Orphanet, Paris, France.
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30
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Bian R, Liu N, Xu Y, Su Z, Chai L, Bernardo A, St Amand P, Fritz A, Zhang G, Rupp J, Akhunov E, Jordan KW, Bai G. Quantitative trait loci for rolled leaf in a wheat EMS mutant from Jagger. Theor Appl Genet 2023; 136:52. [PMID: 36912970 DOI: 10.1007/s00122-023-04284-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
Two QTLs with major effects on rolled leaf trait were consistently detected on chromosomes 1A (QRl.hwwg-1AS) and 5A (QRl.hwwg-5AL) in the field experiments. Rolled leaf (RL) is a morphological strategy to protect plants from dehydration under stressed field conditions. Identification of quantitative trait loci (QTLs) underlining RL is essential to breed drought-tolerant wheat cultivars. A mapping population of 154 recombinant inbred lines was developed from the cross between JagMut1095, a mutant of Jagger, and Jagger to identify quantitative trait loci (QTLs) for the RL trait. A linkage map of 3106 cM was constructed with 1003 unique SNPs from 21 wheat chromosomes. Two consistent QTLs were identified for RL on chromosomes 1A (QRl.hwwg-1AS) and 5A (QRl.hwwg-5AL) in all field experiments. QRl.hwwg-1AS explained 24-56% of the phenotypic variation and QRl.hwwg-5AL explained up to 20% of the phenotypic variation. The combined percent phenotypic variation associated with the two QTLs was up to 61%. Analyses of phenotypic and genotypic data of recombinants generated from heterogeneous inbred families of JagMut1095 × Jagger delimited QRl.hwwg-1AS to a 6.04 Mb physical interval. This work lays solid foundation for further fine mapping and map-based cloning of QRl.hwwg-1AS.
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Affiliation(s)
- Ruolin Bian
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Na Liu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- Henan Agricultural University, Zhengzhou, 450002, Henan Province, China
| | - Yuzhou Xu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Zhenqi Su
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- China Agricultural University, Beijing, 100083, China
| | - Lingling Chai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
- China Agricultural University, Beijing, 100083, China
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Guorong Zhang
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Jessica Rupp
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Katherine W Jordan
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA.
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Hecht I, Weiner C, Kotlyar A, Shoshany N, Pras E. Micro chromosomal deletions at the NYS7 locus and autosomal dominant nystagmus. Exp Eye Res 2023; 230:109459. [PMID: 37001852 DOI: 10.1016/j.exer.2023.109459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/13/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023]
Abstract
Nystagmus is an ocular condition characterized by bilateral involuntary ocular oscillation which can severely affect vision. When not associated with other ocular or systemic diseases, it is referred to as idiopathic or congenital motor nystagmus (CMN). Genome-wide linkage studies have previously identified several loci associated with CMN, however the genes responsible for some of these loci have yet to be identified. We have examined a large, five-generation family with autosomal dominant CMN. Our purpose was to characterize the clinical manifestations and reveal the molecular basis of the disease in this family. In addition to full ophthalmic examination and imaging, molecular analysis included copy number variation analysis, linkage studies, and Sanger sequencing. Expression analyses of candidate genes was done by real-time PCR. Of the 68 family members, 27 subjects in five-generations had CMN, in line with an autosomal dominant inheritance pattern. Molecular analysis was performed on 27 members, 15 of them affected by CMN. Copy number variation analysis using array comparative genomic hybridization (aCGH) revealed a novel deletion located on 1q32 (NYS7) among affected individuals. Linkage analysis using polymorphic markers demonstrated full segregation with a heterozygous haplotype in all affected patients, with a LOD score of >5. Sanger sequencing of affected subjects revealed a novel deletion of 732,526 bp in the linkage interval. No protein-coding genes exist within the deleted region; however, the deletion disrupts topologically associated domains encompassing the gene NR5A2 and the non-protein coding MIR181A. Both are strongly associated with other genes expressed in the retina such as PROX1, which in turn is also associated with genes related to nystagmus such as PAX6. We therefore hypothesized that the deletion might affect NR5A2 and MIR181A expression, causing CMN. Expression analysis by real-time PCR showed significantly lower expression of NR5A2, and significantly higher expression of PROX1 among patients compared with controls. To conclude, among a large five-generation family with autosomal dominant CMN, a large deletion in the interval of NYS7 was linked with the disease. No protein-coding genes exist inside the deleted region, and so the exact mechanism in which CMN is caused is uncertain. Based on topological association and expression analyses we suggest a possible mechanism for the pathogenesis.
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Affiliation(s)
- Idan Hecht
- Department of Ophthalmology, Shamir Medical Center (formerly Assaf-Harofeh), Tzrifin, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Matlow's Ophthalmo-Genetics Laboratory, Department of Ophthalmology, Shamir Medical Center (formerly Assaf-Harofeh), Tzrifin, Israel.
| | - Chen Weiner
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Matlow's Ophthalmo-Genetics Laboratory, Department of Ophthalmology, Shamir Medical Center (formerly Assaf-Harofeh), Tzrifin, Israel
| | - Alina Kotlyar
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Matlow's Ophthalmo-Genetics Laboratory, Department of Ophthalmology, Shamir Medical Center (formerly Assaf-Harofeh), Tzrifin, Israel
| | - Nadav Shoshany
- Department of Ophthalmology, Shamir Medical Center (formerly Assaf-Harofeh), Tzrifin, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Matlow's Ophthalmo-Genetics Laboratory, Department of Ophthalmology, Shamir Medical Center (formerly Assaf-Harofeh), Tzrifin, Israel
| | - Eran Pras
- Department of Ophthalmology, Shamir Medical Center (formerly Assaf-Harofeh), Tzrifin, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Matlow's Ophthalmo-Genetics Laboratory, Department of Ophthalmology, Shamir Medical Center (formerly Assaf-Harofeh), Tzrifin, Israel
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Li C, Binaghi M, Pichon V, Cannarozzi G, Brandão de Freitas L, Hanemian M, Kuhlemeier C. Tight genetic linkage of genes causing hybrid necrosis and pollinator isolation between young species. Nat Plants 2023; 9:420-432. [PMID: 36805038 PMCID: PMC10027609 DOI: 10.1038/s41477-023-01354-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/19/2023] [Indexed: 05/18/2023]
Abstract
The mechanisms of reproductive isolation that cause phenotypic diversification and eventually speciation are a major topic of evolutionary research. Hybrid necrosis is a post-zygotic isolation mechanism in which cell death develops in the absence of pathogens. It is often due to the incompatibility between proteins from two parents. Here we describe a unique case of hybrid necrosis due to an incompatibility between loci on chromosomes 2 and 7 between two pollinator-isolated Petunia species. Typical immune responses as well as endoplasmic reticulum stress responses are induced in the necrotic line. The locus on chromosome 2 encodes ChiA1, a bifunctional GH18 chitinase/lysozyme. The enzymatic activity of ChiA1 is dispensable for the development of necrosis. We propose that the extremely high expression of ChiA1 involves a positive feedback loop between the loci on chromosomes 2 and 7. ChiA1 is tightly linked to major genes involved in the adaptation to different pollinators, a form of pre-zygotic isolation. This linkage of pre- and post-zygotic barriers strengthens reproductive isolation and probably contributes to rapid diversification and speciation.
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Affiliation(s)
- Chaobin Li
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Marta Binaghi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Vivien Pichon
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gina Cannarozzi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Chemistry/Biology/Pharmacy Information Center, ETH Zürich, Zürich, Switzerland
| | - Loreta Brandão de Freitas
- Department of Genetics, Laboratory of Molecular Evolution, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mathieu Hanemian
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France.
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
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Sengupta S. Perspectives on Evolving Gene Therapy for X-Linked Retinitis Pigmentosa. JAMA Ophthalmol 2023; 141:283-284. [PMID: 36757711 DOI: 10.1001/jamaophthalmol.2022.6436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Du Z, Peng Y, Zhang G, Chen L, Jiang S, Kang Z, Zhao J. Direct Evidence Demonstrates that Puccinia striiformis f. sp. tritici Infects Susceptible Barberry to Complete Sexual Cycle in Autumn. Plant Dis 2023; 107:771-783. [PMID: 35939748 DOI: 10.1094/pdis-08-22-1750-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wheat stripe rust is an airborne and destructive disease caused by a heteroecious rust fungus Puccinia striiformis f. sp. tritici (Pst). Studies have demonstrated that the rust pathogen accomplishes sexual reproduction on susceptible barberry under natural conditions in spring, whereas Pst infection on barberry is still in blank in other seasons. In late October 2016, aecial production on barberry shrubs were observed in Linzhi, Tibet, China. Therefore, experimental tests were conducted to verify the existence of sexual cycles of Pst in this season. By inoculating 52 aecial clusters from 30 rusted barberry leaves, four Pst samples, T1 to T4, were successfully recovered from the rusted barberry shrubs. Sixty-five single uredinium (SU) isolates were derived from the four Pst samples. Based on virulence tests on the Chinese differential hosts, T1 to T4 samples were unknown races and showed mixed reactions on some differentials. Twenty-one known races and 44 unknown races belonging to five race groups were identified among the 65 SU isolates. Meanwhile, the 65 SU isolates produced 26 various virulence patterns (VPs; called VP1-VP26) on 25 single Yr gene lines and 15 multilocus genotypes (MLGs) at nine simple sequence repeat marker loci. Clustering analysis showed similar lineage among subpopulations and different lineage between subpopulations. Linkage disequilibrium analysis indicated that the SU population was produced sexually. This study first reported that Pst infects susceptible barberry to complete sexual reproduction in autumn. The results update the knowledge of disease cycle and management of wheat stripe rust and contribute to the understanding of rust genetic diversity in Tibet.
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Affiliation(s)
- Zhimin Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuelin Peng
- Department of Plant Sciences, Agricultural and Animal Husbandry College of Tibet University, Linzhi, Tibet 86000, China
| | - Gensheng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Chen
- Extension Center for Agricultural Technology, Agriculture Department of Tibetan Autonomous Region, Tibet, China
| | - Shuchang Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Shan T, Li Y, Pang S. Identification of a genomic region linked with sex determination of Undaria pinnatifida (Alariaceae) through genomic resequencing and genetic linkage analyses of a segregating gametophyte family. J Phycol 2023; 59:193-203. [PMID: 36330991 DOI: 10.1111/jpy.13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Different from the traditional knowledge about kelp, three sexual phenotypes (female, male, and monoecious) exist in the haploid gametophytes of Undaria pinnatifida. However, the sex-determining mechanisms remain unknown. Genetic linkage mapping is an efficient tool to identify sex-linked regions. In the present study, we resequenced a segregating gametophyte family based on the male genome of U. pinnatifida. A high-density genetic linkage map was constructed using 9887 SNPs, with an average distance of 0.41 cM between adjacent SNPs. On the basis of this genetic map and using the composite interval mapping method, we identified 62 SNPs significantly linked with the sexual phenotype. They were located at a position of 67.67 cM on the linkage group 23, corresponding to a physical range of 14.67 Mbp on the HiC_Scaffold_23 of the genome. Reanalysis of the previous specific length amplified fragment sequencing data according to the reference genome led to the identification of a sex-linked genomic region that encompassed the above-mentioned 14.67 Mbp region. Hence, this overlapped genomic range was likely the sex-determining region. Within this region, 129 genes were retrieved and 39 of them were annotated with explicit function, including the potential male sex-determining gene-encoding high mobility group (HMG) domain protein. Relative expression analysis of the HMG gene showed that its expression was higher in male gametophytes during the vegetative phase and monoecious gametophytes during both the vegetative and gametogenesis phases, but significantly lower in male gametophytes during the gametogenesis phase. These results provide a foundation for deciphering the sex-determining mechanism of U. pinnatifida.
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Affiliation(s)
- Tifeng Shan
- 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
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Yuqian 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaojun Pang
- 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
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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Abstract
Hybrid chains are a combination of ubiquitin (Ub) and Ub-like (UbL) proteins, expanding on the finely tuned Ub code. To decipher this intricate code, understanding of its assembly, architecture, as well as specific interactors of these Ub/UbL hybrid chains are important, warranting the development of suitable reagents. Here, we describe the chemical methodology to access linkage specific non-hydrolyzable Ub-NEDD8-based chains endowed with an affinity handle in all possible combinations of K48 hybrid chain dimers between Ub and NEDD8.
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Affiliation(s)
- David A Pérez Berrocal
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Monique P C Mulder
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands.
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Waltho A, Sommer T. Getting to the Root of Branched Ubiquitin Chains: A Review of Current Methods and Functions. Methods Mol Biol 2023; 2602:19-38. [PMID: 36446964 DOI: 10.1007/978-1-0716-2859-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nearly 20 years since the first branched ubiquitin (Ub) chains were identified by mass spectrometry, our understanding of these chains and their function is still evolving. This is due to the limitations of classical Ub research techniques in identifying these chains and the vast complexity of potential branched chains. Considering only lysine or N-terminal methionine attachment sites, there are already 28 different possible branch points. Taking into account recently discovered ester-linked ubiquitination, branch points of more than two linkage types, and the higher-order chain structures within which branch points exist, the diversity of branched chains is nearly infinite. This review breaks down the complexity of these chains into their general functions, what we know so far about the different linkage combinations, branched chain-optimized methodologies, and the future perspectives of branched chain research.
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Affiliation(s)
- Anita Waltho
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Thomas Sommer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin-Buch, Germany.
- Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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Dai W, Yu H, Liu K, Chengxu Y, Yan J, Zhang C, Xi N, Liu H, Xiangchen C, Zou C, Zhang M, Gao S, Pan G, Ma L, Shen Y. Combined linkage mapping and association analysis uncovers candidate genes for 25 leaf-related traits across three environments in maize. Theor Appl Genet 2023; 136:12. [PMID: 36662253 DOI: 10.1007/s00122-023-04285-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Combined linkage and association analysis revealed five co-localized genetic loci across multiple environments. The key gene Zm00001d026491 was further verified to influence leaf length by candidate gene association analysis. Leaf morphology and number determine the canopy structure and thus affect crop yield. Herein, the genetic basis and key genes for 25 leaf-related traits, including leaf lengths (LL), leaf widths (LW), and leaf areas (LA) of eight continuous leaves under the tassel, and the number of leaves above the primary ear (LAE), were dissected by using an association panel and a biparental population. Using an intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, 290 quantitative trait loci (QTL) controlling these traits were detected across different locations, among which 115 QTL were individually repeatedly identified in at least two environments. Using the association panel, 165 unique significant single-nucleotide polymorphisms (SNPs) were associated with target traits (P < 2.15E-06), of which 35 were separately detected across multiple environments. In total, 42 pleiotropic QTL/SNPs (pQTL/SNPs) were responsible for at least two of the LL, LW, LA, and LAE traits across multiple environments. Combining the QTL mapping and association study, five unique SNPs were located within the confidence intervals of seven QTL, and 77 genes were identified based on the linkage disequilibrium regions of co-localized SNP loci. Gene-based association studies verified that the intragenic variants in the candidate gene Zm00001d026491 influenced LL of the third leaf counted from the top node. These findings will provide vital information to understanding the genetic basis of leaf-related traits and help to cultivate maize varieties with ideal plant architecture.
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Affiliation(s)
- Wei Dai
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hong Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujuan Chengxu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaquan Yan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Na Xi
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoyang Xiangchen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minyan Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Zeng J, Li M, Qiu H, Xu Y, Feng B, Kou F, Xu X, Razzaq MK, Gai J, Wang Y, Xing G. Identification of QTLs and joint QTL segments of leaflet traits at different canopy layers in an interspecific RIL population of soybean. Theor Appl Genet 2022; 135:4261-4275. [PMID: 36203035 DOI: 10.1007/s00122-022-04216-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
A leaflet trait on different canopy layers may have different QTLs; leaflet trait QTLs may cluster to form joint QTL segments; all canopy layer QTLs form a complete QTL system for a leaflet trait. As the main part of the plant canopy structure, leaf/leaflet size and shape affect the plant architecture and yield. To explore the leaflet trait QTL system, a population composed of 199 recombinant inbred lines derived from Changling (annual wild, narrow leaflet) and Yiqianli (landrace, broad leaflet) with their parents was tested for leaflet length (LL), width (LW) and length to width (LLW). The population was genotyped with specific-locus amplified fragment sequencing (SLAF-seq) and applied for linkage mapping of the leaflet traits. The results showed that the leaflet traits varied greatly even within a plant, which supported a stratified leaflet sampling strategy to evaluate these traits at top, middle and bottom canopy layers. Altogether, 13 LL, 10 LW and 9 LLW in a total of 32 plus 3 duplicated QTLs were identified, in which, 17 QTLs were new ones, and 48.6%, 28.6% and 22.8% of QTLs were from the top, middle and bottom layers, respectively, indicating the genetic importance of the top layer leaves. Since a leaflet trait may have layer-specific QTLs, all layer QTLs form a complete QTL system. Five QTL clusters each with their QTL supporting intervals overlapped were designated as joint QTL segments (JQSs). In JQS-16, with its linkage map further validated using PCR markers, two QTLs, qLW-16-1 and qLLW-16-1 of the top layer leaflet, were identified six QTL·times. Six candidate genes were predicted, with Glyma.16G127900 as the most potential one for LW and LLW. Three PCR markers, Gm16PAV0653, BARCSOYSSR_16_0796 and YC-16-3, were suggested for marker-assisted selection for LW and LLW in JQS-16.
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Affiliation(s)
- Jian Zeng
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Meng Li
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Hongmei Qiu
- Jilin Academy of Agricultural Sciences & National Engineering Research Center for Soybean, Changchun, China
| | - Yufei Xu
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Beibei Feng
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Fangyuan Kou
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Xianchao Xu
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Khuram Razzaq
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
| | - Yueqiang Wang
- Jilin Academy of Agricultural Sciences & National Engineering Research Center for Soybean, Changchun, China.
| | - Guangnan Xing
- Soybean Research Institute & MARA National Center for Soybean Improvement & MARA Key Laboratory of Biology and Genetic Improvement of Soybean & National Key Laboratory for Crop Genetics and Germplasm Enhancement & Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China.
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40
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Liang Z, Xi N, Liu H, Liu P, Xiang C, Zhang C, Zou C, Cheng X, Yu H, Zhang M, Chen Z, Pan G, Yuan G, Gao S, Ma L, Shen Y. An Integration of Linkage Mapping and GWAS Reveals the Key Genes for Ear Shank Length in Maize. Int J Mol Sci 2022; 23:ijms232315073. [PMID: 36499409 PMCID: PMC9740654 DOI: 10.3390/ijms232315073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Ear shank length (ESL) has significant effects on grain yield and kernel dehydration rate in maize. Herein, linkage mapping and genome-wide association study were combined to reveal the genetic architecture of maize ESL. Sixteen quantitative trait loci (QTL) were identified in the segregation population, among which five were repeatedly detected across multiple environments. Meanwhile, 23 single nucleotide polymorphisms were associated with the ESL in the association panel, of which four were located in the QTL identified by linkage mapping and were designated as the population-common loci. A total of 42 genes residing in the linkage disequilibrium regions of these common variants and 12 of them were responsive to ear shank elongation. Of the 12 genes, five encode leucine-rich repeat receptor-like protein kinases, proline-rich proteins, and cyclin11, respectively, which were previously shown to regulate cell division, expansion, and elongation. Gene-based association analyses revealed that the variant located in Cyclin11 promoter affected the ESL among different lines. Cyclin11 showed the highest expression in the ear shank 15 days after silking among diverse tissues of maize, suggesting its role in modulating ESL. Our study contributes to the understanding of the genetic mechanism underlying maize ESL and genetic modification of maize dehydration rate and kernel yield.
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Zhu L, Wang Y, Zhang Z, Hu D, Wang Z, Hu J, Ma C, Yang L, Sun S, Li Y. Chromosomal fragment deletion in APRR2-repeated locus modulates the dark stem color in Cucurbita pepo. Theor Appl Genet 2022; 135:4277-4288. [PMID: 36098750 DOI: 10.1007/s00122-022-04217-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Cp4.1LG15g03420 (CpDsc-1), which encodes a two-component response regulator-like protein (APRR2) in the nucleus, influences dark green stem formation in Cucurbita pepo by regulating the chlorophyll content. Stem color is an important agronomic trait in zucchini (Cucurbita pepo) for robust seeding and high yield. However, the gene controlling the stem color has not been characterized. In this study, we identified a single locus accounting for the dark green stem color of C. pepo (CpDsc-1). Genetic analysis of this trait in segregated populations derived from two parental lines (line 296 with dark green stems and line 274 with light green stems) revealed that stem color was controlled by a single dominant gene (dark green vs. light green). In bulked segregant analysis, CpDsc-1 was mapped to a 2.09-Mb interval on chromosome 15. This region was further narrowed to 65.2 kb using linkage analysis of the F2 population. Sequencing analysis revealed a 14 kb deletion between Cp4.1LG15g03420 and Cp4.1LG15g03360; these two genes both encoded a two-component response regulator-like protein (APRR2). The incomplete structures of the two APRR2 genes and abnormal chloroplasts in line 274 might be the main cause of the light green phenotype. Gene expression pattern analysis showed that only Cp4.1LG15g03420 was upregulated in line 296. Subcellular localization analysis indicated that Cp4.1LG15g03420 was a nuclear gene. Furthermore, a co-dominant marker, G4563 (93% accuracy rate), and a co-segregation marker, Fra3, were established in 111 diverse germplasms; both of these markers were tightly linked with the color trait. This study provided insights into chlorophyll regulation mechanisms and revealed the markers valuable for marker-assisted selection in future zucchini breeding.
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Affiliation(s)
- Lei Zhu
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Yong Wang
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China
| | - Zhenli Zhang
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Deju Hu
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Zanlin Wang
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Jianbin Hu
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Changsheng Ma
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Luming Yang
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China
| | - Shouru Sun
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China.
- International Joint Laboratory of Horticultural Biology, College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, China.
| | - Yanman Li
- Henan Engineering Technology Research Center of Germplasm Innovation and Utilization of Melon Crops, Henan Agricultural University, Zhengzhou, China.
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42
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Vervalle JA, Costantini L, Lorenzi S, Pindo M, Mora R, Bolognesi G, Marini M, Lashbrooke JG, Tobutt KR, Vivier MA, Roodt-Wilding R, Grando MS, Bellin D. A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip. Theor Appl Genet 2022; 135:4371-4390. [PMID: 36271055 PMCID: PMC9734222 DOI: 10.1007/s00122-022-04225-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
We present a high-density integrated map for grapevine, allowing refinement and improved understanding of the grapevine genome, while demonstrating the applicability of the Vitis18K SNP chip for linkage mapping. The improvement of grapevine through biotechnology requires identification of the molecular bases of target traits by studying marker-trait associations. The Vitis18K SNP chip provides a useful genotyping tool for genome-wide marker analysis. Most linkage maps are based on single mapping populations, but an integrated map can increase marker density and show order conservation. Here we present an integrated map based on three mapping populations. The parents consist of the well-known wine cultivars 'Cabernet Sauvignon', 'Corvina' and 'Rhine Riesling', the lesser-known wine variety 'Deckrot', and a table grape selection, G1-7720. Three high-density population maps with an average inter-locus gap ranging from 0.74 to 0.99 cM were developed. These maps show high correlations (0.9965-0.9971) with the reference assembly, containing only 93 markers with large order discrepancies compared to expected physical positions, of which a third is consistent across multiple populations. Moreover, the genetic data aid the further refinement of the grapevine genome assembly, by anchoring 104 yet unanchored scaffolds. From these population maps, an integrated map was constructed which includes 6697 molecular markers and reduces the inter-locus gap distance to 0.60 cM, resulting in the densest integrated map for grapevine thus far. A small number of discrepancies, mainly of short distance, involve 88 markers that remain conflictual across maps. The integrated map shows similar collinearity to the reference assembly (0.9974) as the single maps. This high-density map increases our understanding of the grapevine genome and provides a useful tool for its further characterization and the dissection of complex traits.
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Affiliation(s)
- Jessica A Vervalle
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
- ARC Infruitec-Nietvoorbij, Stellenbosch, 7599, South Africa
| | - Laura Costantini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Silvia Lorenzi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Riccardo Mora
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Giada Bolognesi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Martina Marini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Justin G Lashbrooke
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Ken R Tobutt
- ARC Infruitec-Nietvoorbij, Stellenbosch, 7599, South Africa
| | - Melané A Vivier
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Maria Stella Grando
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Center Agriculture Food and Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy.
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Lu Q, Yu X, Wang H, Yu Z, Zhang X, Zhao Y. Construction of ultra-high-density genetic linkage map of a sorghum-sudangrass hybrid using whole genome resequencing. PLoS One 2022; 17:e0278153. [PMID: 36445892 PMCID: PMC9707794 DOI: 10.1371/journal.pone.0278153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
The sorghum-sudangrass hybrid is a vital annual gramineous herbage. Few reports exist on its ultra-high-density genetic map. In this study, we sought to create an ultra-high-density genetic linkage map for this hybrid to strengthen its functional genomics research and genetic breeding. We used 150 sorghum-sudangrass hybrid F2 individuals and their parents (scattered ear sorghum and red hull sudangrass) for high-throughput sequencing on the basis of whole genome resequencing. In total, 1,180.66 Gb of data were collected. After identification, filtration for integrity, and partial segregation, over 5,656 single nucleotide polymorphism markers of high quality were detected. An ultra-high-density genetic linkage map was constructed using these data. The markers covered approximately 2,192.84 cM of the map with average marker intervals of 0.39 cM. The length ranged from 115.39 cM to 264.04 cM for the 10 linkage groups. Currently, this represents the first genetic linkage map of this size, number of molecular markers, density, and coverage for sorghum-sudangrass hybrid. The findings of this study provide valuable genome-level information on species evolution and comparative genomics analysis and lay the foundation for further research on quantitative trait loci fine mapping and gene cloning and marker-assisted breeding of important traits in sorghum-sudangrass hybrids.
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Affiliation(s)
- Qianqian Lu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaoxia Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Huiting Wang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhuo Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- * E-mail:
| | - Xia Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Yaqi Zhao
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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Taagen E, Jordan K, Akhunov E, Sorrells ME, Jannink JL. If It Ain't Broke, Don't Fix It: Evaluating the Effect of Increased Recombination on Response to Selection for Wheat Breeding. G3 Genes|Genomes|Genetics 2022; 12:6798772. [PMID: 36331396 PMCID: PMC9713416 DOI: 10.1093/g3journal/jkac291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
Abstract
Meiotic recombination is a source of allelic diversity, but the low frequency and biased distribution of crossovers that occur during meiosis limits the genetic variation available to plant breeders. Simulation studies previously identified that increased recombination frequency can retain more genetic variation and drive greater genetic gains than wildtype recombination. Our study was motivated by the need to define desirable recombination intervals in regions of the genome with fewer crossovers. We hypothesized that deleterious variants, which can negatively impact phenotypes and occur at higher frequencies in low recombining regions where they are linked in repulsion with favorable loci, may offer a signal for positioning shifts of recombination distributions. Genomic selection breeding simulation models based on empirical wheat data were developed to evaluate increased recombination frequency and changing recombination distribution on response to selection. Comparing high and low values for a range of simulation parameters identified that few combinations retained greater genetic variation and fewer still achieved higher genetic gain than wildtype. More recombination was associated with loss of genomic prediction accuracy, which outweighed the benefits of disrupting repulsion linkages. Irrespective of recombination frequency or distribution and deleterious variant annotation, enhanced response to selection under increased recombination required polygenic trait architecture, high heritability, an initial scenario of more repulsion than coupling linkages, and greater than six cycles of genomic selection. Altogether, the outcomes of this research discourage a controlled recombination approach to genomic selection in wheat as a more efficient path to retaining genetic variation and increasing genetic gains compared to existing breeding methods.
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Affiliation(s)
- Ella Taagen
- Corresponding author: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Katherine Jordan
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66502, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | - Mark E Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY 14853, USA
| | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY 14853, USA
- USDA-ARS, R.W. Holley Center, Cornell University, Ithaca, NY 14853, USA
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Best NB, McSteen P. Mapping Maize Mutants Using Bulked-Segregant Analysis and Next-Generation Sequencing. Curr Protoc 2022; 2:e591. [PMID: 36350247 DOI: 10.1002/cpz1.591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Forward genetics is used to identify the genetic basis for a phenotype. The approach involves identifying a mutant organism exhibiting a phenotype of interest and then mapping the causative locus or gene. Bulked-segregant analysis (BSA) is a quick and effective approach to map mutants using pools of mutants and wild-type plants from a segregating population to identify linkage of the mutant phenotype, and this approach has been successfully used in plants. Traditional linkage mapping approaches are outdated and time intensive, and can be very difficult. With the highly evolved development and reduction in cost of high-throughput sequencing, this new approach combined with BSA has become extremely effective in multiple plant species, including Zea mays (maize). While the approach is incredibly powerful, careful experimental design, bioinformatic mapping techniques, and interpretation of results are important to obtain the desired results in an effective and timely manner. Poor design of a mapping population, limitations in bioinformatic experience, and inadequate understanding of sequence data are limitations of these approaches for the researcher. Here, we describe a straightforward protocol for mapping mutations responsible for a phenotype of interest in maize, using high-throughput sequencing and BSA. Specifically, we discuss relevant aspects of developing a mutant mapping population. This is followed by a detailed protocol for DNA preparation and analysis of short-read sequences to map and identify candidate causative mutations responsible for the mutant phenotype of interest. We provide command-line and perl scripts to complete the bioinformatic analysis of the mutant sequence data. This protocol lays out the design of the BSA, bioinformatic approaches, and interpreting the sequencing data. These methods are very adaptable to any forward genetics experiment and provide a step-by-step approach to identifying the genetic basis of a maize mutant phenotype. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Bulked-segregant analysis and high-throughput sequencing to map maize mutants.
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Affiliation(s)
- Norman B Best
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri
| | - Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri
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Li L, Liu J, Gong H, Zhao Y, Luo J, Sun Z, Li T. A dominant gene Ihrl1 is tightly linked to and inhibits the gene Ndhrl1 mediating nitrogen-dependent hypersensitive reaction-like phenotype in wheat. Theor Appl Genet 2022; 135:3563-3570. [PMID: 36030437 DOI: 10.1007/s00122-022-04200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Identification and mapping of an inhibitor of Ndhrl1 mediating nitrogen-dependent hypersensitive reaction-like phenotype in wheat. Hypersensitive reaction-like (HRL) traits are characteristic of spontaneous lesions including yellowish spots, brown spots or white-stripe that appeared randomly and dispersedly on all the leaves in the absence of plant pathogens. Our previous studies have shown that the wheat line P7001 showed an HRL trait at low nitrogen supply, and this trait was controlled by the gene Ndhrl1 (Nitrogen-dependent hypersensitive reaction-like 1). In order to investigate the robustness of the trait expression mediated by Ndhrl1 under different genetic backgrounds, seven genetic populations, with P7001 being the common female parent, were constructed and analyzed. F1 plants from six of the seven combinations showed HRL trait and Ndhrl1 segregated in a dominant way of HRL: non-HRL = 3:1 in the six populations (F2). Exceptionally, the F1 plants of P7001/Fielder combination showed non-HRL trait and HRL trait in the F2 population showed a contrasting recessive segregation ratio of HRL: non-HRL = 1:3, suggesting Fielder may have another HRL-related gene. Using 55 K SNP array and PCR-based markers, the HRL-related gene in Fielder was mapped to an interval of 5.63-12.91 Mb on the short arm of chromosome 2B with the flanking markers Yzu660R075552 and Yzu660F075941. A recombinant with genomic region of Fielder at Ndhrl1 locus showing HRL trait demonstrated that Fielder also harbored Ndhrl1 same as P7001. Thus, Fielder carries a single dominant suppressor of Ndhrl1, designated as Ihrl1 (Inhibitor of hypersensitive reaction-like). Interestingly, Ihrl1 is tightly linked to Ndhrl1 and may be also involved in nitrogen metabolic and (or) signaling pathways.
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Affiliation(s)
- Lei Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Jiaqi Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Hao Gong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Yang Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Jinbiao Luo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Zhengxi Sun
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Tao Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Zhang Y, Miao H, Wang C, Zhang J, Zhang X, Shi X, Xie S, Li T, Deng P, Wang C, Chen C, Zhang H, Ji W. Genetic identification of the pleiotropic gene Tasg-D1/2 affecting wheat grain shape by regulating brassinolide metabolism. Plant Sci 2022; 323:111392. [PMID: 35868348 DOI: 10.1016/j.plantsci.2022.111392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/08/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Improving yield potential is a major goal of wheat breeding that depends on identifying key genetic loci. In this study, two residual heterozygous line RHL351- and RHL78-derived populations were employed for genetic linkage map construction and QTL detection. Two genetic populations indicated a robust grain-size QTL between Marker6 and Marker10. It covered a 95.54-99.38 Mb physical interval and was named Qpleio.nwafu.3D, containing the candidate gene Tasg (TraesCS3D02G137200). Intriguingly, RNA-seq analysis and sequencing revealed two different allelic variants in Tasg, named Tasg-D1 (G>A) and Tasg-D2 (C>G), respectively. Although the relationship between Tasg-D1 and grain size had been demonstrated previously, here we provided the first genetic evidence that C/G allelic variation in Tasg-D2 was associated with grain shape and size through a newly developed dCAPS marker. In addition, transcriptome comparison indicated that Tasg-D1/2 might primarily contribute to significant expression differences in brassinolide (BR) metabolism-related genes rather than those related to BR responses in developing grains and spikes. Our study provided new evidence and a breeder-friendly dCAPS marker for improving grain size through the selection of Tasg, as well as a basis to understand Tasg function in the future.
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Affiliation(s)
- Yaoyuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Hanxiao Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Junjie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiangyu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiaoxi Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Songfeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China.
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48
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Michael TP. Core circadian clock and light signaling genes brought into genetic linkage across the green lineage. Plant Physiol 2022; 190:1037-1056. [PMID: 35674369 PMCID: PMC9516744 DOI: 10.1093/plphys/kiac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The circadian clock is conserved at both the level of transcriptional networks as well as core genes in plants, ensuring that biological processes are phased to the correct time of day. In the model plant Arabidopsis (Arabidopsis thaliana), the core circadian SHAQKYF-type-MYB (sMYB) genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and REVEILLE (RVE4) show genetic linkage with PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7, respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis enabled tracing this genetic linkage back to Amborella trichopoda, a sister lineage to the angiosperm, and identifying an additional evolutionarily conserved genetic linkage in light signaling genes. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7, and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of angiosperm families representing distinct whole-genome duplication and fractionation events. Soybean (Glycine max) maintained all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase, in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae), such as maize (Zea mays), where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The environmental robustness model is put forward, suggesting that evolutionarily conserved genetic linkages ensure superior microhabitat pollinator synchrony, while wide-hybrids or unlinking the genes, as seen in the grasses, result in heterosis, adaptation, and colonization of new ecological niches.
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Guan P, Li X, Zhuang L, Wu B, Huang J, Zhao J, Qiao L, Zheng J, Hao C, Zheng X. Genetic dissection of lutein content in common wheat via association and linkage mapping. Theor Appl Genet 2022; 135:3127-3141. [PMID: 35951035 DOI: 10.1007/s00122-022-04175-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Genetic architecture controlling grain lutein content of common wheat was investigated through an integration of genome-wide association study (GWAS) and linkage analysis. Putative candidate genes involved in carotenoid metabolism and regulation were identified, which provide a basis for gene cloning and development of nutrient-enriched wheat varieties through molecular breeding. Lutein, known as 'the eye vitamin', is an important component of wheat nutritional and end-use quality. However, the genetic manipulation of grain lutein content (LUC) in common wheat has not previously been well studied. Here, quantitative trait loci (QTL) associated with the LUC measured by high performance liquid chromatography (HPLC) were first identified by integrating a genome-wide association study (GWAS) and linkage mapping. A Chinese wheat mini-core collection (MCC) of 262 accessions and a doubled haploid (DH) population derived from Jinchun 7 and L1219 were genotyped using the 90K SNP array. A total of 124 significant marker-trait associations (MTAs) on all 21 wheat chromosomes except for 1A, 4D, and 5B that formed 58 QTL were detected. Among them, six stable QTL were identified on chromosomes 2AL, 2DS, 3BL, 3DL, 7AL, and 7BS. Meanwhile, three of the ten QTL identified in the DH population, QLuc.5A.1 and QLuc.5A.2 on chromosome 5AL and QLuc.6A.2 on 6AS, were stable and independently explained 5.58-10.86% of the phenotypic variation. The QLuc.6A.2 region colocalized with two MTAs identified by GWAS. Moreover, 71 carotenoid metabolism-related candidate genes were identified, and the allelic effects were analyzed in the MCC panel based on the 90K array. Results revealed that the genes CYP97A3 (Chr. 6B) and CCD1 (Chr. 5A) were significantly associated with LUC. Additionally, the gene PSY3 (QLuc.5A.1) and several candidate genes involved in the methylerythritol 4-phosphate (MEP) pathways colocalized with stable QTL regions. The present study provides potential targets for future functional gene exploration and molecular breeding in common wheat.
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Affiliation(s)
- Panfeng Guan
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Wheat Research, Shanxi Agricultural University/State Key Laboratory of Sustainable Dryland Agriculture, Taiyuan, 030031, China
| | - Xiaohua Li
- Institute of Wheat Research, Shanxi Agricultural University/State Key Laboratory of Sustainable Dryland Agriculture, Taiyuan, 030031, China
| | - Lei Zhuang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bangbang Wu
- Institute of Wheat Research, Shanxi Agricultural University/State Key Laboratory of Sustainable Dryland Agriculture, Taiyuan, 030031, China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University/State Key Laboratory of Sustainable Dryland Agriculture, Taiyuan, 030031, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University/State Key Laboratory of Sustainable Dryland Agriculture, Taiyuan, 030031, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University/State Key Laboratory of Sustainable Dryland Agriculture, Taiyuan, 030031, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University/State Key Laboratory of Sustainable Dryland Agriculture, Taiyuan, 030031, China.
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50
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Bernardo R. Covariance between nonrelatives in maize. Heredity (Edinb) 2022; 129:155-160. [PMID: 35676495 PMCID: PMC9411190 DOI: 10.1038/s41437-022-00548-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 11/09/2022] Open
Abstract
The covariance between relatives is a tenet in quantitative genetics, but the covariance between nonrelatives in crops has not been studied. My objective was to determine if a covariance between nonrelatives is present in maize (Zea mays L.). The germplasm comprised 272 maize lines that were previously genotyped with 28,626 single nucleotide polymorphism (SNP) markers. Pairs of unrelated lines were identified on the basis of their membership probabilities in five subpopulations. The covariance between nonrelatives was assessed as the regression of phenotypic similarity on SNP similarity between unrelated lines. Out of 77 regressions, seven were significant at a 5% false discovery rate: anthesis and silking dates in unrelated B73 and Oh43 lines; plant height and ear height in unrelated Oh43 and PH207 lines; oil in unrelated A321 and Mo17 lines; starch in unrelated B73 and PH207 lines; and protein in unrelated B73 and Mo17 lines. The latter covariance was negative, and this negative covariance between nonrelatives was attributed to the subpopulations having different linkage phases between the markers and underlying causal variants. Overall, the results indicated that a covariance between nonrelatives in maize is not ubiquitous but is sometimes present for specific traits and for certain groups of unrelated individuals. I propose that the covariance between nonrelatives and the covariance between relatives be combined into a generalized covariance between individuals, thus giving a unified framework for expressing the resemblance regardless of the degree of relatedness.
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Affiliation(s)
- Rex Bernardo
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Buford Circle, Saint Paul, MN, 55108, USA.
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