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Long M, Wang B, Yang Z, Lu X. Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle. Animals (Basel) 2024; 14:2181. [PMID: 39123707 PMCID: PMC11311069 DOI: 10.3390/ani14152181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the future profitability of the dairy sector. Registered body conformation traits are reliable and cost-effective tools for use in national cattle breeding selection programs. These traits are significantly related to the production, longevity, mobility, health, fertility, and environmental adaptation of dairy cows. Therefore, they can be considered indirect indicators of economically important traits in dairy cows. Utilizing efficacious genetic methods, such as genome-wide association studies (GWASs), allows for a deeper understanding of the genetic architecture of complex traits through the identification and application of genetic markers. In the current review, we summarize information on candidate genes and genomic regions associated with body conformation traits in dairy cattle worldwide. The manuscript also reviews the importance of body conformation, the relationship between body conformation traits and other traits, heritability, influencing factors, and the genetics of body conformation traits. The information on candidate genes related to body conformation traits provided in this review may be helpful in selecting potential genetic markers for the genetic improvement of body conformation traits in dairy cattle.
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Affiliation(s)
- Mingxue Long
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (M.L.); (Z.Y.)
| | - Bo Wang
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China;
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (M.L.); (Z.Y.)
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (M.L.); (Z.Y.)
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Qadri QR, Lai X, Zhao W, Zhang Z, Zhao Q, Ma P, Pan Y, Wang Q. Exploring the Interplay between the Hologenome and Complex Traits in Bovine and Porcine Animals Using Genome-Wide Association Analysis. Int J Mol Sci 2024; 25:6234. [PMID: 38892420 PMCID: PMC11172659 DOI: 10.3390/ijms25116234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/25/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Genome-wide association studies (GWAS) significantly enhance our ability to identify trait-associated genomic variants by considering the host genome. Moreover, the hologenome refers to the host organism's collective genetic material and its associated microbiome. In this study, we utilized the hologenome framework, called Hologenome-wide association studies (HWAS), to dissect the architecture of complex traits, including milk yield, methane emissions, rumen physiology in cattle, and gut microbial composition in pigs. We employed four statistical models: (1) GWAS, (2) Microbial GWAS (M-GWAS), (3) HWAS-CG (hologenome interaction estimated using COvariance between Random Effects Genome-based restricted maximum likelihood (CORE-GREML)), and (4) HWAS-H (hologenome interaction estimated using the Hadamard product method). We applied Bonferroni correction to interpret the significant associations in the complex traits. The GWAS and M-GWAS detected one and sixteen significant SNPs for milk yield traits, respectively, whereas the HWAS-CG and HWAS-H each identified eight SNPs. Moreover, HWAS-CG revealed four, and the remaining models identified three SNPs each for methane emissions traits. The GWAS and HWAS-CG detected one and three SNPs for rumen physiology traits, respectively. For the pigs' gut microbial composition traits, the GWAS, M-GWAS, HWAS-CG, and HWAS-H identified 14, 16, 13, and 12 SNPs, respectively. We further explored these associations through SNP annotation and by analyzing biological processes and functional pathways. Additionally, we integrated our GWA results with expression quantitative trait locus (eQTL) data using transcriptome-wide association studies (TWAS) and summary-based Mendelian randomization (SMR) methods for a more comprehensive understanding of SNP-trait associations. Our study revealed hologenomic variability in agriculturally important traits, enhancing our understanding of host-microbiome interactions.
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Affiliation(s)
- Qamar Raza Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (Q.R.Q.); (P.M.)
| | - Xueshuang Lai
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310030, China; (X.L.); (W.Z.); (Z.Z.); (Y.P.)
| | - Wei Zhao
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310030, China; (X.L.); (W.Z.); (Z.Z.); (Y.P.)
| | - Zhenyang Zhang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310030, China; (X.L.); (W.Z.); (Z.Z.); (Y.P.)
| | - Qingbo Zhao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China;
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (Q.R.Q.); (P.M.)
| | - Yuchun Pan
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310030, China; (X.L.); (W.Z.); (Z.Z.); (Y.P.)
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China
| | - Qishan Wang
- Key Laboratory of Dairy Cow Genetic Improvement and Milk Quality Research of Zhejiang Province, College of Animal Science, Zhejiang University, Hangzhou 310030, China; (X.L.); (W.Z.); (Z.Z.); (Y.P.)
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya 572000, China
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Thakur NR, Gorthy S, Vemula A, Odeny DA, Ruperao P, Sargar PR, Mehtre SP, Kalpande HV, Habyarimana E. Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains. Sci Rep 2024; 14:12729. [PMID: 38830906 PMCID: PMC11148041 DOI: 10.1038/s41598-024-63308-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/27/2024] [Indexed: 06/05/2024] Open
Abstract
Sorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study. Both micronutrients exhibited good variability with respective ranges of 22.09-52.55 ppm and 17.92-43.16 ppm. Significant marker-trait associations were identified on chromosomes 1, 3, and 5. Two major effect SNPs (S01_72265728 and S05_58213541) explained 35% and 32% of Fe and Zn phenotypic variance, respectively. The SNP S01_72265728 was identified in the cytochrome P450 gene and showed a positive effect on Fe accumulation in the kernel, while S05_58213541 was intergenic near Sobic.005G134800 (zinc-binding ribosomal protein) and showed negative effect on Zn. Tissue-specific in silico expression analysis resulted in higher levels of Sobic.003G350800 gene product in several tissues such as leaf, root, flower, panicle, and stem. Sobic.005G188300 and Sobic.001G463800 were expressed moderately at grain maturity and anthesis in leaf, root, panicle, and seed tissues. The candidate genes expressed in leaves, stems, and grains will be targeted to improve grain and stover quality. The haplotypes identified will be useful in forward genetics breeding.
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Affiliation(s)
- Niranjan Ravindra Thakur
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | - Sunita Gorthy
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - AnilKumar Vemula
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
| | - Pramod Ramchandra Sargar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | | | - Hirakant V Kalpande
- Vasantrao Naik Marathwada Agriculture University, Parbhani, Maharashtra, India
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India.
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Istaitieh M, Yoosefzadeh Najafabadi M, Edwards AM, Todd J, Van Acker R, Rajcan I. Genetic study for seed germination and shattering in Euphorbia lagascae in response to different seed treatments. Heliyon 2024; 10:e27975. [PMID: 38560240 PMCID: PMC10979140 DOI: 10.1016/j.heliyon.2024.e27975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 02/24/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Euphorbia lagascae Spreng is a promising emerging oilseed crop, with its seed oil accounting for approximately 50% of the seed weight. Euphorbia oil contains a significant amount of vernolic acid, comprising two-thirds of its composition, which boasts various industrial applications, including acting as a stabilizer-plasticizer and natural dye. However, this species was known to have a high degree of seed-shattering and a low germination rate, which act as two important barriers to large-scale production and exploitation. Therefore, the objective of this study is to determine the genetic control of seed germination and seed-shattering traits in order to develop a reliable pipeline that would be applicable for industries and breeders to select superior E. lagascae lines and design a robust breeding scheme in a short time at reduced labor costs. For this objective, five different wild-type genotypes of E. lagascae that demonstrated high germination potential were crossed with an ethyl methanesulfonate (EMS) mutant genotype that produces non-shattering capsules. The F2 populations from two successful crosses (A and B) were separated into three different treated groups for seed germination evaluation and to study the segregation of 200 individuals per F2 population. The three treatments were: light, gibberellic acid (GA3), and control treatment. Consequently, plants treated with approximately 250 μmol/m2/s of light showed significant improvement in germination up to 75% in cross A and 82.4 % in cross B compared with the control plants and the group treated with 0.05% GA3. According to the chi-square test results, the inheritance pattern of seed germination in response to light treatment follows a 3:1 segregation ratio between germinated and non-germinated seeds, indicating a dominant gene action in the F2 generation. The same conclusion was followed for the shattering trait in the group treated with light, which was also simply inherited as a 3:1 ratio for shattering vs. non-shattering capsules. Our results emphasize the importance and significance of light treatment in producing uniform populations through acceptable germination and shattering resistance of the mutant genotypes of E. lagascae. This is the first report of light treatment that significantly improved seed germination of E. lagascae, which may enhance efforts in the development of this new industrial crop as a feedstock for vernolic acid production.
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Affiliation(s)
- Maram Istaitieh
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - A. Michelle Edwards
- Office of Research, Ontario Agri-Food Innovation Alliance, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jim Todd
- Ontario Ministry of Agriculture, Food and Rural Affairs, 1283 Blueline Rd, Simcoe, ON, N3Y 4K3, Canada
| | - Rene Van Acker
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Zhao Z, Liang C, Zhang W, Yang Y, Bi Q, Yu H, Wang L. Genome-wide association analysis identifies a candidate gene controlling seed size and yield in Xanthoceras sorbifolium Bunge. HORTICULTURE RESEARCH 2024; 11:uhad243. [PMID: 38225982 PMCID: PMC10788774 DOI: 10.1093/hr/uhad243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
Yellow horn (Xanthoceras sorbifolium Bunge) is a woody oilseed tree species whose seed oil is rich in unsaturated fatty acids and rare neuronic acids, and can be used as a high-grade edible oil or as a feedstock for biodiesel production. However, the genetic mechanisms related to seed yield in yellow horn are not well elucidated. This study identified 2 164 863 SNP loci based on 222 genome-wide resequencing data of yellow horn germplasm. We conducted genome-wide association study (GWAS) analysis on three core traits (hundred-grain weight, single-fruit seed mass, and single-fruit seed number) that influence seed yield for the years 2022 and 2020, and identified 399 significant SNP loci. Among these loci, the Chr10_24013014 and Chr10_24012613 loci caught our attention due to their consistent associations across multiple analyses. Through Sanger sequencing, we validated the genotypes of these two loci across 16 germplasms, confirming their consistency with the GWAS analysis results. Downstream of these two significant loci, we identified a candidate gene encoding an AP2 transcription factor protein, which we named XsAP2. RT-qPCR analysis revealed high expression of the XsAP2 gene in seeds, and a significant negative correlation between its expression levels and seed hundred-grain weight, as well as single-fruit seed mass, suggesting its potential role in the normal seed development process. Transgenic Arabidopsis lines with the overexpressed XsAP2 gene exhibited varying degrees of reduction in seed size, number of seeds per silique, and number of siliques per plant compared with wild-type Arabidopsis. Combining these results, we hypothesize that the XsAP2 gene may have a negative regulatory effect on seed yield of yellow horn. These results provide a reference for the molecular breeding of high-yielding yellow horn.
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Affiliation(s)
- Ziquan Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Chongjun Liang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
- College of Forestry, Hainan University, Haikou 570228, China
| | - Wei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Yingying Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Haiyan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry Chinese Academy of Forestry, Beijing 100091, China
- College of Forestry, Hainan University, Haikou 570228, China
- College of Forestry, Northwest A&F University, Yangling 712100, China
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Ma H. Editorial for the Special Issue "Genetics Studies on Wheat". Genes (Basel) 2023; 14:1761. [PMID: 37761901 PMCID: PMC10530819 DOI: 10.3390/genes14091761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 09/29/2023] Open
Abstract
Wheat (Triticum aestivum L [...].
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Affiliation(s)
- Hongxiang Ma
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center of Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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7
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Haidar S, Lackey S, Charette M, Yoosefzadeh-Najafabadi M, Gahagan AC, Hotte T, Belzile F, Rajcan I, Golshani A, Morrison MJ, Cober ER, Samanfar B. Genome-wide analysis of cold imbibition stress in soybean, Glycine max. FRONTIERS IN PLANT SCIENCE 2023; 14:1221644. [PMID: 37670866 PMCID: PMC10476531 DOI: 10.3389/fpls.2023.1221644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/07/2023]
Abstract
In Canada, the length of the frost-free season necessitates planting crops as early as possible to ensure that the plants have enough time to reach full maturity before they are harvested. Early planting carries inherent risks of cold water imbibition (specifically less than 4°C) affecting seed germination. A marker dataset developed for a previously identified Canadian soybean GWAS panel was leveraged to investigate the effect of cold water imbibition on germination. Seed from a panel of 137 soybean elite cultivars, grown in the field at Ottawa, ON, over three years, were placed on filter paper in petri dishes and allowed to imbibe water for 16 hours at either 4°C or 20°C prior to being transferred to a constant 20°C. Observations on seed germination, defined as the presence of a 1 cm radicle, were done from day two to seven. A three-parameter exponential rise to a maximum equation (3PERM) was fitted to estimate germination, time to the one-half maximum germination, and germination uniformity for each cultivar. Genotype-by-sequencing was used to identify SNPs in 137 soybean lines, and using genome-wide association studies (GWAS - rMVP R package, with GLM, MLM, and FarmCPU as methods), haplotype block analysis, and assumed linkage blocks of ±100 kbp, a threshold for significance was established using the qvalue package in R, and five significant SNPs were identified on chromosomes 1, 3, 4, 6, and 13 for maximum germination after cold water imbibition. Percent of phenotypic variance explained (PVE) and allele substitution effect (ASE) eliminated two of the five candidate SNPs, leaving three QTL regions on chromosomes 3, 6, and 13 (Chr3-3419152, Chr6-5098454, and Chr13-29649544). Based on the gene ontology (GO) enrichment analysis, 14 candidate genes whose function is predicted to include germination and cold tolerance related pathways were identified as candidate genes. The identified QTLs can be used to select future soybean cultivars tolerant to cold water imbibition and mitigate risks associated with early soybean planting.
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Affiliation(s)
- Siwar Haidar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Simon Lackey
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | | | - A. Claire Gahagan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Thomas Hotte
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Francois Belzile
- Department of Phytology, Institut de Biologie Intégrative et des Systèmes (IBIS), Université de Laval, Quebec City, QC, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Malcolm J. Morrison
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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Abdi H, Alipour H, Bernousi I, Jafarzadeh J, Rodrigues PC. Identification of novel putative alleles related to important agronomic traits of wheat using robust strategies in GWAS. Sci Rep 2023; 13:9927. [PMID: 37336905 DOI: 10.1038/s41598-023-36134-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023] Open
Abstract
Principal component analysis (PCA) is widely used in various genetics studies. In this study, the role of classical PCA (cPCA) and robust PCA (rPCA) was evaluated explicitly in genome-wide association studies (GWAS). We evaluated 294 wheat genotypes under well-watered and rain-fed, focusing on spike traits. First, we showed that some phenotypic and genotypic observations could be outliers based on cPCA and different rPCA algorithms (Proj, Grid, Hubert, and Locantore). Hubert's method provided a better approach to identifying outliers, which helped to understand the nature of these samples. These outliers led to the deviation of the heritability of traits from the actual value. Then, we performed GWAS with 36,000 single nucleotide polymorphisms (SNPs) based on the traditional approach and two robust strategies. In the conventional approach and using the first three components of cPCA as population structure, 184 and 139 marker-trait associations (MTAs) were identified for five traits in well-watered and rain-fed environments, respectively. In the first robust strategy and when rPCA was used as population structure in GWAS, we observed that the Hubert and Grid methods identified new MTAs, especially for yield and spike weight on chromosomes 7A and 6B. In the second strategy, we followed the classical and robust principal component-based GWAS, where the first two PCs obtained from phenotypic variables were used instead of traits. In the recent strategy, despite the similarity between the methods, some new MTAs were identified that can be considered pleiotropic. Hubert's method provided a better linear combination of traits because it had the most MTAs in common with the traditional approach. Newly identified SNPs, including rs19833 (5B) and rs48316 (2B), were annotated with important genes with vital biological processes and molecular functions. The approaches presented in this study can reduce the misleading GWAS results caused by the adverse effect of outlier observations.
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Affiliation(s)
- Hossein Abdi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Iraj Bernousi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
| | - Jafar Jafarzadeh
- Dryland Agricultural Research Institute (DARI), Agriculture Research, Education and Extension Organization (AREEO), Maragheh, Iran
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Yoosefzadeh Najafabadi M, Hesami M, Rajcan I. Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1956. [PMID: 37653871 PMCID: PMC10221147 DOI: 10.3390/plants12101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/30/2023]
Abstract
Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian heredity is not applicable, known as non-Mendelian heredity. This type of inheritance can be influenced by several factors besides the genetic architecture of the plant and its breeding potential. Therefore, exploring various non-Mendelian heredity mechanisms, their prevalence in plants, and the implications for plant breeding is of paramount importance to accelerate the pace of crop improvement. In this review, we examine the current understanding of non-Mendelian heredity in plants, including the mechanisms, inheritance patterns, and applications in plant breeding, provide an overview of the various forms of non-Mendelian inheritance (including epigenetic inheritance, cytoplasmic inheritance, hybrid vigor, and LOH), explore insight into the implications of non-Mendelian heredity in plant breeding, and the potential it holds for future research.
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Affiliation(s)
| | | | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.Y.N.); (M.H.)
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Oteng-Frimpong R, Karikari B, Sie EK, Kassim YB, Puozaa DK, Rasheed MA, Fonceka D, Okello DK, Balota M, Burow M, Ozias-Akins P. Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut ( Arachis hypogaea L.) germplasm. FRONTIERS IN PLANT SCIENCE 2023; 13:1076744. [PMID: 36684745 PMCID: PMC9849250 DOI: 10.3389/fpls.2022.1076744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Early leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in ≤ 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at ± 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.
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Affiliation(s)
- Richard Oteng-Frimpong
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Emmanuel Kofi Sie
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Yussif Baba Kassim
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Doris Kanvenaa Puozaa
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Masawudu Abdul Rasheed
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Daniel Fonceka
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation àla Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Thiès, Senegal
| | - David Kallule Okello
- Oil Crops Research Program, National Semi-Arid Resources Research Institute (NaSARRI), Soroti, Uganda
| | - Maria Balota
- School of Plant and Environmental Sciences, Tidewater Agricultural Research and Extension Center (AREC), Virginia Tech, Suffolk, VA, United States
| | - Mark Burow
- Texas A&M AgriLife Research and Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Peggy Ozias-Akins
- Institute of Plant Breeding Genetics and Genomics, University of Georgia, Tifton, GA, United States
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