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Sallam A, Awadalla RA, Elshamy MM, Börner A, Heikal YM. Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population. Comput Struct Biotechnol J 2024; 23:870-882. [PMID: 38356657 PMCID: PMC10864764 DOI: 10.1016/j.csbj.2024.01.020] [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: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.
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Affiliation(s)
- Ahmed Sallam
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Rawan A. Awadalla
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Maha M. Elshamy
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Andreas Börner
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
| | - Yasmin M. Heikal
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
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Zhang H, Tang Y, Yue Y, Chen Y. Advances in the evolution research and genetic breeding of peanut. Gene 2024; 916:148425. [PMID: 38575102 DOI: 10.1016/j.gene.2024.148425] [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: 11/29/2023] [Revised: 03/15/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Peanut is an important cash crop used in oil, food and feed in our country. The rapid development of sequencing technology has promoted the research on the related aspects of peanut genetic breeding. This paper reviews the research progress of peanut origin and evolution, genetic breeding, molecular markers and their applications, genomics, QTL mapping and genome selection techniques. The main problems of molecular genetic breeding in peanut research worldwide include: the narrow genetic resources of cultivated species, unstable genetic transformation and unclear molecular mechanism of important agronomic traits. Considering the severe challenges regarding the supply of edible oil, and the main problems in peanut production, the urgent research directions of peanut are put forward: The de novo domestication and the exploitation of excellent genes from wild resources to improve modern cultivars; Integration of multi-omics data to enhance the importance of big data in peanut genetics and breeding; Cloning the important genes related to peanut agronomic traits and analyzing their fine regulation mechanisms; Precision molecular design breeding and using gene editing technology to accurately improve the key traits of peanut.
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Affiliation(s)
- Hui Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Yueyi Tang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Yunlai Yue
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yong Chen
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Bhad PG, Mondal S, Badigannavar AM. Molecular tagging of seed size using MITE markers in an induced large seed mutant with higher cotyledon cell size in groundnut. 3 Biotech 2024; 14:56. [PMID: 38298555 PMCID: PMC10825088 DOI: 10.1007/s13205-023-03909-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024] Open
Abstract
A large seed mutant, TG 89 having a 76.7% increment in hundred kernel weight in comparison to its parent TG 26, was isolated from an electron beam-induced mutagenized population. Studies based on environmental scanning electron microscopy of both parent and mutant revealed that the mutant seed cotyledon had significantly bigger cell size than parent. A mapping population with 122 F2 plants derived from the mutant and a distant normal seed genotype (ICGV 15007) was utilized to map the QTL associated with higher HKW. Bulk segregant analysis revealed putative association of three markers with this mutant large seed trait. Further, genotyping of F2 individuals with polymorphic markers detected 14 linkage groups with a map distance of 1053 cM. QTL analysis revealed a significant additive major QTL for the mutant large seed trait on linkage group A05 explaining 12.7% phenotypic variation for the seed size. This QTL was located between flanking markers AhTE333 and AhTE810 having a map interval of 4.7 cM which corresponds to 90.65 to 107.24 Mbp in A05 chromosome, respectively. Within this genomic fragment, an ortholog of the BIG SEEDS 1 gene was found at 102,476,137 bp. Real-time PCR revealed down-regulation of this BIG SEEDS 1 gene in the mutant indicating a loss of function mutation giving rise to a large seed phenotype. This QTL was validated in 11 advanced breeding lines having large seed size from this mutant but with varied genetic backgrounds. This validation showcased a highly promising selection accuracy of 90.9% for the marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03909-0.
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Affiliation(s)
- Poonam Gajanan Bhad
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Anand M. Badigannavar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
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Conde S, Rami JF, Okello DK, Sambou A, Muitia A, Oteng-Frimpong R, Makweti L, Sako D, Faye I, Chintu J, Coulibaly AM, Miningou A, Asibuo JY, Konate M, Banla EM, Seye M, Djiboune YR, Tossim HA, Sylla SN, Hoisington D, Clevenger J, Chu Y, Tallury S, Ozias-Akins P, Fonceka D. The groundnut improvement network for Africa (GINA) germplasm collection: a unique genetic resource for breeding and gene discovery. G3 (BETHESDA, MD.) 2023; 14:jkad244. [PMID: 37875136 PMCID: PMC10755195 DOI: 10.1093/g3journal/jkad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 08/22/2023] [Accepted: 10/03/2023] [Indexed: 10/26/2023]
Abstract
Cultivated peanut or groundnut (Arachis hypogaea L.) is a grain legume grown in many developing countries by smallholder farmers for food, feed, and/or income. The speciation of the cultivated species, that involved polyploidization followed by domestication, greatly reduced its variability at the DNA level. Mobilizing peanut diversity is a prerequisite for any breeding program for overcoming the main constraints that plague production and for increasing yield in farmer fields. In this study, the Groundnut Improvement Network for Africa assembled a collection of 1,049 peanut breeding lines, varieties, and landraces from 9 countries in Africa. The collection was genotyped with the Axiom_Arachis2 48K SNP array and 8,229 polymorphic single nucleotide polymorphism (SNP) markers were used to analyze the genetic structure of this collection and quantify the level of genetic diversity in each breeding program. A supervised model was developed using dapc to unambiguously assign 542, 35, and 172 genotypes to the Spanish, Valencia, and Virginia market types, respectively. Distance-based clustering of the collection showed a clear grouping structure according to subspecies and market types, with 73% of the genotypes classified as fastigiata and 27% as hypogaea subspecies. Using STRUCTURE, the global structuration was confirmed and showed that, at a minimum membership of 0.8, 76% of the varieties that were not assigned by dapc were actually admixed. This was particularly the case of most of the genotype of the Valencia subgroup that exhibited admixed genetic heritage. The results also showed that the geographic origin (i.e. East, Southern, and West Africa) did not strongly explain the genetic structure. The gene diversity managed by each breeding program, measured by the expected heterozygosity, ranged from 0.25 to 0.39, with the Niger breeding program having the lowest diversity mainly because only lines that belong to the fastigiata subspecies are used in this program. Finally, we developed a core collection composed of 300 accessions based on breeding traits and genetic diversity. This collection, which is composed of 205 genotypes of fastigiata subspecies (158 Spanish and 47 Valencia) and 95 genotypes of hypogaea subspecies (all Virginia), improves the genetic diversity of each individual breeding program and is, therefore, a unique resource for allele mining and breeding.
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Affiliation(s)
- Soukeye Conde
- ISRA, Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- UMR AGAP, CIRAD, 34398 Montpellier, France
- CIRAD, INRAE, AGAP, University Montpellier, Institut Agro, 34398 Montpellier, France
- F.S.T., Département de B.V., Université Cheikh Anta Diop, BP 5005 Dakar, Senegal
| | - Jean-François Rami
- UMR AGAP, CIRAD, 34398 Montpellier, France
- CIRAD, INRAE, AGAP, University Montpellier, Institut Agro, 34398 Montpellier, France
| | - David K Okello
- National Semi-Arid Resources Research Institute-Serere, PO Box 56, Kampala, Uganda
| | - Aissatou Sambou
- ISRA, Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
| | - Amade Muitia
- Mozambique Agricultural Research Institute (Instituto de Investigação Agrária de Moçambique), Northeast Zonal Centre, Nampula Research Station, PO Box 1922, Nampula, Mozambique
| | - Richard Oteng-Frimpong
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, PO Box 52, Tamale, Ghana
| | - Lutangu Makweti
- Zambia Agriculture Research Institute (ZARI), PO Box 510089, Chipata, Zambia
| | - Dramane Sako
- Institut d’Economie Rurale (IER), Centre Régional de Recherche Agronomique (CRRA), BP 281 Kayes, Mali
| | - Issa Faye
- ISRA, Institut Sénégalais de Recherches Agricoles, Centre National de Recherche Agronomique, BP 53 Bambey, Sénégal
| | - Justus Chintu
- Chitedze Agricultural Research Service, PO Box 158, Lilongwe, Malawi
| | - Adama M Coulibaly
- Institut National de Recherche Agronomique du Niger (INRAN), BP 240 Maradi, Niger
| | - Amos Miningou
- INERA, CREAF, 01 BP 476 Ouagadougou 01, Burkina Faso
| | - James Y Asibuo
- Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI), P.O. Box 3785, Kumasi, Ghana
| | - Moumouni Konate
- INERA, DRREA-Ouest, 01 BP 910 Bobo Dioulasso 01, Burkina Faso
| | - Essohouna M Banla
- Institut Togolais de Recherche Agronomique (ITRA), 13BP267 Lome, Togo
| | - Maguette Seye
- ISRA, Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
| | - Yvette R Djiboune
- ISRA, Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
| | - Hodo-Abalo Tossim
- ISRA, Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
| | - Samba N Sylla
- F.S.T., Département de B.V., Université Cheikh Anta Diop, BP 5005 Dakar, Senegal
| | - David Hoisington
- Feed the Future Innovation Lab for Peanut, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| | - Josh Clevenger
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ye Chu
- Institute of Plant Breeding Genetics and Genomics and Department of Horticulture, College of Agricultural and Environmental Sciences, University of Georgia, Tifton, GA 31793, USA
| | - Shyam Tallury
- Plant Genetic Resources Conservation Unit, Griffin, GA 30223, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding Genetics and Genomics and Department of Horticulture, College of Agricultural and Environmental Sciences, University of Georgia, Tifton, GA 31793, USA
| | - Daniel Fonceka
- ISRA, Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- UMR AGAP, CIRAD, 34398 Montpellier, France
- CIRAD, INRAE, AGAP, University Montpellier, Institut Agro, 34398 Montpellier, France
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Kim K, Jun TH, Ha BK, Wang S, Sun H. New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits. BMC Bioinformatics 2023; 24:381. [PMID: 37817069 PMCID: PMC10563219 DOI: 10.1186/s12859-023-05505-8] [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: 02/10/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Identification of pleiotropic variants associated with multiple phenotypic traits has received increasing attention in genetic association studies. Overlapping genetic associations from multiple traits help to detect weak genetic associations missed by single-trait analyses. Many statistical methods were developed to identify pleiotropic variants with most of them being limited to quantitative traits when pleiotropic effects on both quantitative and qualitative traits have been observed. This is a statistically challenging problem because there does not exist an appropriate multivariate distribution to model both quantitative and qualitative data together. Alternatively, meta-analysis methods can be applied, which basically integrate summary statistics of individual variants associated with either a quantitative or a qualitative trait without accounting for correlations among genetic variants. RESULTS We propose a new statistical selection method based on a unified selection score quantifying how a genetic variant, i.e., a pleiotropic variant associates with both quantitative and qualitative traits. In our extensive simulation studies where various types of pleiotropic effects on both quantitative and qualitative traits were considered, we demonstrated that the proposed method outperforms the existing meta-analysis methods in terms of true positive selection. We also applied the proposed method to a peanut dataset with 6 quantitative and 2 qualitative traits, and a cowpea dataset with 2 quantitative and 6 qualitative traits. We were able to detect some potentially pleiotropic variants missed by the existing methods in both analyses. CONCLUSIONS The proposed method is able to locate pleiotropic variants associated with both quantitative and qualitative traits. It has been implemented into an R package 'UNISS', which can be downloaded from http://github.com/statpng/uniss.
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Affiliation(s)
- Kipoong Kim
- Department of Statistic, Pusan National University, 46241, Busan, Korea
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, 50463, Miryang, Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, 61186, Gwangju, Korea
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, 10032, USA
| | - Hokeun Sun
- Department of Statistic, Pusan National University, 46241, Busan, Korea.
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Yan L, Song W, Wang Z, Yu D, Sudini H, Kang Y, Lei Y, Huai D, Chen Y, Wang X, Wang Q, Liao B. Dissection of the Genetic Basis of Resistance to Stem Rot in Cultivated Peanuts ( Arachis hypogaea L.) through Genome-Wide Association Study. Genes (Basel) 2023; 14:1447. [PMID: 37510351 PMCID: PMC10378806 DOI: 10.3390/genes14071447] [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: 06/17/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Peanut (Arachis hypogaea) is an important oilseed and cash crop worldwide, contributing an important source of edible oil and protein for human nutrition. However, the incidence of stem rot disease caused by Athelia rolfsii poses a major challenge to peanut cultivation, resulting in significant yield losses. In this study, a panel of 202 peanut accessions was evaluated for their resistance to stem rot by inoculating plants in the field with A. rolfsii-infested oat grains in three environments. The mean disease index value of each environment for accessions in subsp. fasitigiate and subsp. hypogaea showed no significant difference. Accessions from southern China displayed the lowest disease index value compared to those from other ecological regions. We used whole-genome resequencing to analyze the genotypes of the accessions and to identify significant SNPs associated with stem rot resistance through genome-wide association study (GWAS). A total of 121 significant SNPs associated with stem rot resistance in peanut were identified, with phenotypic variation explained (PVE) ranging from 12.23% to 15.51%. A total of 27 candidate genes within 100 kb upstream and downstream of 23 significant SNPs were annotated, which have functions related to recognition, signal transduction, and defense response. These significant SNPs and candidate genes provide valuable information for further validation and molecular breeding to improve stem rot resistance in peanut.
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Affiliation(s)
- Liying Yan
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Wanduo Song
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Zhihui Wang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Dongyang Yu
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Hari Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Yanping Kang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yong Lei
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Dongxin Huai
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yuning Chen
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xin Wang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Qianqian Wang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Boshou Liao
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agricultural and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Gangurde SS, Pasupuleti J, Parmar S, Variath MT, Bomireddy D, Manohar SS, Varshney RK, Singam P, Guo B, Pandey MK. Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut. Front Genet 2023; 14:1128182. [PMID: 37007937 PMCID: PMC10061104 DOI: 10.3389/fgene.2023.1128182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Seed size is not only a yield-related trait but also an important measure to determine the commercial value of groundnut in the international market. For instance, small size is preferred in oil production, whereas large-sized seeds are preferred in confectioneries. In order to identify the genomic regions associated with 100-seed weight (HSW) and shelling percentage (SHP), the recombinant inbred line (RIL) population (Chico × ICGV 02251) of 352 individuals was phenotyped for three seasons and genotyped with an Axiom_Arachis array containing 58K SNPs. A genetic map with 4199 SNP loci was constructed, spanning a map distance of 2708.36 cM. QTL analysis identified six QTLs for SHP, with three consistent QTLs on chromosomes A05, A08, and B10. Similarly, for HSW, seven QTLs located on chromosomes A01, A02, A04, A10, B05, B06, and B09 were identified. BIG SEED locus and spermidine synthase candidate genes associated with seed weight were identified in the QTL region on chromosome B09. Laccase, fibre protein, lipid transfer protein, senescence-associated protein, and disease-resistant NBS-LRR proteins were identified in the QTL regions associated with shelling percentage. The associated markers for major-effect QTLs for both traits successfully distinguished between the small- and large-seeded RILs. QTLs identified for HSW and SHP can be used for developing potential selectable markers to improve the cultivars with desired seed size and shelling percentage to meet the demands of confectionery industries.
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Affiliation(s)
- Sunil S. Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
- USDA-ARS, Crops Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Janila Pasupuleti
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sejal Parmar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Murali T. Variath
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Deekshitha Bomireddy
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surendra S. Manohar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Baozhu Guo
- USDA-ARS, Crops Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
- *Correspondence: Manish K. Pandey,
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8
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Liu Y, Shao L, Zhou J, Li R, Pandey MK, Han Y, Cui F, Zhang J, Guo F, Chen J, Shan S, Fan G, Zhang H, Seim I, Liu X, Li X, Varshney RK, Li G, Wan S. Genomic insights into the genetic signatures of selection and seed trait loci in cultivated peanut. J Adv Res 2022; 42:237-248. [PMID: 36513415 PMCID: PMC9788939 DOI: 10.1016/j.jare.2022.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Cultivated peanut (Arachis hypogaea L.) is an important oil crop for human nutrition and is cultivated in >100 countries. However, the present knowledge of its genomic diversity, evolution, and loci related to the seed traits is limited. OBJECTIVES Our study intended to (1) uncover the population structure and the demographic history of peanuts, (2) identify signatures of selection that occurred during peanut improvement breeding, and (3) detect and verify the functions of candidate genes associated with seed traits. METHODS We explored the population relationship and the evolution of peanuts using a largescale single nucleotide polymorphism dataset generated from the genome-wide resequencing of 203 cultivated peanuts. Genetic diversity and genomic scan analyses were applied to identify selective loci for genomic-selection breeding. Genome-wide association studies, transgenic experiments, and RNA-seq were employed to identify the candidate genes associated with seed traits. RESULTS Our study revealed that the 203 resequenced accessions were divided into four genetic groups, consistent with their botanical classification. Moreover, the var. peruviana and var. fastigiata subpopulations have diverged to a greater extent than the others, and var. peruviana may be the earliest variant in the evolution from tetraploid ancestors. A recent dramatic expansion in the effective population size of the cultivated peanuts ca. 300-500 years ago was also noted. Selective sweeps underlying quantitative trait loci and genes of seed size, plant architecture, and disease resistance coincide with the major goals of improved peanut breeding compared with the landrace and cultivar populations. Genome-wide association testing with functional analysis led to the identification of two genes involved in seed weight and seed length regulation. CONCLUSION Our study provides valuable information for understanding the genomic diversity and the evolution of peanuts and serves as a genomic basis for improving peanut cultivars.
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Affiliation(s)
- Yiyang Liu
- Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, Shandong Province, China
| | - Libin Shao
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong Province, China
| | - Jing Zhou
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong Province, China
| | - Rongchong Li
- Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, Shandong Province, China
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Yan Han
- College of Life Sciences, Shandong Normal University, Ji’nan 250014, Shandong Province, China
| | - Feng Cui
- Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, Shandong Province, China
| | - Jialei Zhang
- Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, Shandong Province, China
| | - Feng Guo
- Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, Shandong Province, China
| | - Jing Chen
- Shandong Peanut Research Institute, Qingdao 266000, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao 266000, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong Province, China,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - He Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Wenyuan Road, Nanjing 210023, China,School of Biology and Environmental Science, Queensland University of Technology, Brisbane 4000, Australia
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xinguo Li
- Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, Shandong Province, China,Corresponding authors.
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India,The UWA Institute of Agriculture, the University of Western Australia, Perth, WA 6001, Australia,State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, Western Australia, Australia,Corresponding authors.
| | - Guowei Li
- Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, Shandong Province, China,College of Life Sciences, Shandong Normal University, Ji’nan 250014, Shandong Province, China,Corresponding authors.
| | - Shubo Wan
- Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, Shandong Province, China,Corresponding authors.
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