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Pan J, Li X, Fu C, Bian J, Wang Z, Yu C, Liu X, Wang G, Tian R, Song X, Li C, Xia H, Zhao S, Hou L, Gao M, Zi H, Bertioli D, Leal-Bertioli S, Pandey MK, Wang X, Zhao C. High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:69. [PMID: 38441650 DOI: 10.1007/s00122-024-04580-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024]
Abstract
KEY MESSAGE Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance. Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species. In this study, a synthetic amphidiploid (Ipadur) of wild peanuts with high LLS resistance was used to cross with Tifrunner to construct TI population. In total, 200 recombinant inbred lines were collected for whole-genome resequencing. A high-density bin-based genetic linkage map was constructed, which includes 4,809 bin markers with an average inter-bin distance of 0.43 cM. The recombination across cultivated and wild species was unevenly distributed, providing a novel recombination landscape for cultivated-wild Arachis species. Using phenotyping data collected across three environments, 28 QTLs for LLS disease resistance were identified, explaining 4.35-20.42% of phenotypic variation. The major QTL located on chromosome 14, qLLS14.1, could be consistently detected in 2021 Jiyang and 2022 Henan with 20.42% and 12.12% PVE, respectively. A favorable 530-kb chromosome segment derived from Ipadur was identified in the region of qLLS14.1, in which 23 disease resistance proteins were located and six of them showed significant sequence variations between Tifrunner and Ipadur. Allelic variation analysis indicating the 530-kb segment of wild species might contribute to the disease resistance of LLS. These associate genomic regions and candidate resistance genes are of great significance for peanut breeding programs for bringing durable resistance through pyramiding such multiple LLS resistance loci into peanut cultivars.
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Affiliation(s)
- Jiaowen Pan
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaojie Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Chun Fu
- Weifang Academy of Agricultural Sciences, Weifang, 261071, People's Republic of China
| | - Jianxin Bian
- Institute of Advanced Agricultural Science, Peking University, Weifang, 261071, People's Republic of China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, People's Republic of China
| | - Conghui Yu
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaoqin Liu
- Institute of Advanced Agricultural Science, Peking University, Weifang, 261071, People's Republic of China
| | - Guanghao Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaofeng Song
- Weifang Academy of Agricultural Sciences, Weifang, 261071, People's Republic of China
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - Han Xia
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Lei Hou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Meng Gao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, People's Republic of China
| | - Hailing Zi
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Soraya Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
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Chen YJ, Pandey S, Catto M, Leal-Bertioli S, Abney MR, Bag S, Hopkins M, Culbreath A, Srinivasan R. Evaluation of Wild Peanut Species and Their Allotetraploids for Resistance against Thrips and Thrips-Transmitted Tomato Spotted Wilt Orthotospovirus (TSWV). Pathogens 2023; 12:1102. [PMID: 37764910 PMCID: PMC10536083 DOI: 10.3390/pathogens12091102] [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: 07/20/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) causes spotted wilt disease in peanut (Arachis hypogaea L.) and limits yield. Breeding programs have been developing TSWV-resistant cultivars, but availability of sources of resistance against TSWV in cultivated germplasm is extremely limited. Diploid wild Arachis species can serve as important sources of resistance, and despite ploidy barriers (cultivated peanut is tetraploid), their usage in breeding programs is now possible because of the knowledge and development of induced interspecific allotetraploid hybrids. This study screened 10 wild diploid Arachis and six induced allotetraploid genotypes via thrips-mediated TSWV transmission assays and thrips' feeding assays in the greenhouse. Three parameters were evaluated: percent TSWV infection, virus accumulation, and temporal severity of thrips feeding injury. Results indicated that the diploid A. stenosperma accession V10309 and its derivative-induced allotetraploid ValSten1 had the lowest TSWV infection incidences among the evaluated genotypes. Allotetraploid BatDur1 had the lowest thrips-inflicted damage at each week post thrips release, while diploid A. batizocoi accession K9484 and A. duranensis accession V14167 had reduced feeding damage one week post thrips release, and diploids A. valida accession GK30011 and A. batizocoi had reduced feeding damage three weeks post thrips releasethan the others. Overall, plausible TSWV resistance in diploid species and their allotetraploid hybrids was characterized by reduced percent TSWV infection, virus accumulation, and feeding severity. Furthermore, a few diploids and tetraploid hybrids displayed antibiosis against thrips. These results document evidence for resistance against TSWV and thrips in wild diploid Arachis species and peanut-compatible-induced allotetraploids.
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Affiliation(s)
- Yi-Ju Chen
- Department of Entomology, University of Georgia, Griffin, GA 30223, USA; (Y.-J.C.); (S.P.)
| | - Sudeep Pandey
- Department of Entomology, University of Georgia, Griffin, GA 30223, USA; (Y.-J.C.); (S.P.)
| | - Michael Catto
- Department of Entomology, University of Georgia, Athens, GA 30602, USA;
| | - Soraya Leal-Bertioli
- Department of Plant Pathology, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
| | - Mark R. Abney
- Department of Entomology, University of Georgia, Tifton, GA 31794, USA;
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.B.); (A.C.)
| | - Mark Hopkins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.B.); (A.C.)
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Huang R, Li H, Gao C, Yu W, Zhang S. Advances in omics research on peanut response to biotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 14:1101994. [PMID: 37284721 PMCID: PMC10239885 DOI: 10.3389/fpls.2023.1101994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/18/2023] [Indexed: 06/08/2023]
Abstract
Peanut growth, development, and eventual production are constrained by biotic and abiotic stresses resulting in serious economic losses. To understand the response and tolerance mechanism of peanut to biotic and abiotic stresses, high-throughput Omics approaches have been applied in peanut research. Integrated Omics approaches are essential for elucidating the temporal and spatial changes that occur in peanut facing different stresses. The integration of functional genomics with other Omics highlights the relationships between peanut genomes and phenotypes under specific stress conditions. In this review, we focus on research on peanut biotic stresses. Here we review the primary types of biotic stresses that threaten sustainable peanut production, the multi-Omics technologies for peanut research and breeding, and the recent advances in various peanut Omics under biotic stresses, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics and phenomics, for identification of biotic stress-related genes, proteins, metabolites and their networks as well as the development of potential traits. We also discuss the challenges, opportunities, and future directions for peanut Omics under biotic stresses, aiming sustainable food production. The Omics knowledge is instrumental for improving peanut tolerance to cope with various biotic stresses and for meeting the food demands of the exponentially growing global population.
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Affiliation(s)
- Ruihua Huang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Hongqing Li
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Caiji Gao
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
| | - Weichang Yu
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Liaoning Peanut Research Institute, Liaoning Academy of Agricultural Sciences, Fuxing, China
- China Good Crop Company (Shenzhen) Limited, Shenzhen, China
| | - Shengchun Zhang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, China
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Jha UC, Nayyar H, Chattopadhyay A, Beena R, Lone AA, Naik YD, Thudi M, Prasad PVV, Gupta S, Dixit GP, Siddique KHM. Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration. FRONTIERS IN PLANT SCIENCE 2023; 14:1183505. [PMID: 37229109 PMCID: PMC10204772 DOI: 10.3389/fpls.2023.1183505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023]
Abstract
Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Anirudha Chattopadhyay
- Department of Plant Pathology, Pulse Research Station, S.D. Agricultural University SK Nagar, SK Nagar, Gujarat, India
| | - Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University (KAU), Thiruvananthapuram, Kerala, India
| | - Ajaz A. Lone
- Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST)-Kashmir, Srinagar, India
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | | | - Sanjeev Gupta
- Indian Council of Agricultural Research, New Delhi, India
| | - Girish Prasad Dixit
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Kadambot H. M. Siddique
- The University of Western Australia (UWA) Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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Moretzsohn MDC, dos Santos JF, Moraes ARA, Custódio AR, Michelotto MD, Mahrajan N, Leal-Bertioli SCDM, Godoy IJ, Bertioli DJ. Marker-assisted introgression of wild chromosome segments conferring resistance to fungal foliar diseases into peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1139361. [PMID: 37056498 PMCID: PMC10088909 DOI: 10.3389/fpls.2023.1139361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Fungal foliar diseases can severely affect the productivity of the peanut crop worldwide. Late leaf spot is the most frequent disease and a major problem of the crop in Brazil and many other tropical countries. Only partial resistance to fungal diseases has been found in cultivated peanut, but high resistances have been described on the secondary gene pool. METHODS To overcome the known compatibility barriers for the use of wild species in peanut breeding programs, we used an induced allotetraploid (Arachis stenosperma × A. magna)4x, as a donor parent, in a successive backcrossing scheme with the high-yielding Brazilian cultivar IAC OL 4. We used microsatellite markers associated with late leaf spot and rust resistance for foreground selection and high-throughput SNP genotyping for background selection. RESULTS With these tools, we developed agronomically adapted lines with high cultivated genome recovery, high-yield potential, and wild chromosome segments from both A. stenosperma and A. magna conferring high resistance to late leaf spot and rust. These segments include the four previously identified as having QTLs (quantitative trait loci) for resistance to both diseases, which could be confirmed here, and at least four additional QTLs identified by using mapping populations on four generations. DISCUSSION The introgression germplasm developed here will extend the useful genetic diversity of the primary gene pool by providing novel wild resistance genes against these two destructive peanut diseases.
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Affiliation(s)
| | | | | | - Adriana Regina Custódio
- Plant Genetics Laboratory, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | | | - Namrata Mahrajan
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Soraya Cristina de Macedo Leal-Bertioli
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Ignácio José Godoy
- Grain and Fiber Center, Agronomic Institute of Campinas (IAC), Campinas, SP, Brazil
| | - David John Bertioli
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Science, University of Georgia, Athens, GA, United States
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Saxesena RR, Mishra VK, Chand R, Kumar U, Chowdhury AK, Bhati J, Budhlakoti N, Joshi AK. SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat ( Triticum aestivum L.), an Essential Crop for Food Security. Front Genet 2022; 13:859676. [PMID: 35450212 PMCID: PMC9016274 DOI: 10.3389/fgene.2022.859676] [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: 01/21/2022] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
The pathogenic fungus, Bipolaris sorokiniana, that causes spot blotch (SB) disease of wheat, is a major production constraint in the Eastern Gangetic Plains of South Asia and other warm, humid regions of the world. A recombinant inbred line population was developed and phenotyped at three SB-prone locations in India. The single nucleotide polymorphism (SNP) for SB resistance was identified using a bulked segregant RNA-Seq-based approach, referred to as “BSR-Seq.” Transcriptome sequencing of the resistant parent (YS#24), the susceptible parent (YS#58), and their resistant and susceptible bulks yielded a total of 429.67 million raw reads. The bulk frequency ratio (BFR) of SNPs between the resistant and susceptible bulks was estimated, and selection of SNPs linked to resistance was done using sixfold enrichments in the corresponding bulks (BFR >6). With additional filtering criteria, the number of transcripts was further reduced to 506 with 1055 putative polymorphic SNPs distributed on 21 chromosomes of wheat. Based on SNP enrichment on chromosomal loci, five transcripts were found to be associated with SB resistance. Among the five SB resistance-associated transcripts, four were distributed on the 5B chromosome with putative 52 SNPs, whereas one transcript with eight SNPs was present on chromosome 3B. The SNPs linked to the trait were exposed to a tetra-primer ARMS-PCR assay, and an SNP-based allele-specific marker was identified for SB resistance. The in silico study of these five transcripts showed homology with pathogenesis-related genes; the metabolic pathway also exhibits similar results, suggesting their role in the plant defense mechanism.
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Affiliation(s)
- Ravi Ranjan Saxesena
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | | | - Jyotika Bhati
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), Ludhiana, India.,International Maize and Wheat Improvement Center (CIMMYT) and Borlaug Institute for South Asia (BISA), DPS Marg, New Delhi, India
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Impact of Host Resistance to Tomato Spotted Wilt Orthotospovirus in Peanut Cultivars on Virus Population Genetics and Thrips Fitness. Pathogens 2021; 10:pathogens10111418. [PMID: 34832574 PMCID: PMC8625697 DOI: 10.3390/pathogens10111418] [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: 09/30/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/25/2022] Open
Abstract
Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) is a major constraint to peanut production in the southeastern United States. Peanut cultivars with resistance to TSWV have been widely used for over twenty years. Intensive usage of resistant cultivars has raised concerns about possible selection pressure against TSWV and a likelihood of resistance breakdown. Population genetics of TSWV isolates collected from cultivars with varying levels of TSWV resistance was investigated using five TSWV genes. Phylogenetic trees of genes did not indicate host resistance-based clustering of TSWV isolates. Genetic variation in TSWV isolates and neutrality tests suggested recent population expansion. Mutation and purifying selection seem to be the major forces driving TSWV evolution. Positive selection was found in N and RdRp genes but was not influenced by TSWV resistance. Population differentiation occurred between isolates collected from 1998 and 2010 and from 2016 to 2019 but not between isolates from susceptible and resistant cultivars. Evaluated TSWV-resistant cultivars differed, albeit not substantially, in their susceptibility to thrips. Thrips oviposition was reduced, and development was delayed in some cultivars. Overall, no evidence was found to support exertion of selection pressure on TSWV by host resistance in peanut cultivars, and some cultivars differentially affected thrips fitness than others.
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Defense-Related Gene Expression Following an Orthotospovirus Infection Is Influenced by Host Resistance in Arachis hypogaea. Viruses 2021; 13:v13071303. [PMID: 34372510 PMCID: PMC8310252 DOI: 10.3390/v13071303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 12/13/2022] Open
Abstract
Planting resistant cultivars is the most effective tactic to manage the thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) in peanut plants. However, molecular mechanisms conferring resistance to TSWV in resistant cultivars are unknown. In this study, transcriptomes of TSWV-susceptible (SunOleic 97R) and field-resistant (Tifguard) peanut cultivars with and without TSWV infection were assembled and differentially expressed genes (DEGs) were compared. There were 4605 and 2579 significant DEGs in SunOleic 97R and Tifguard, respectively. Despite the lower number of DEGs in Tifguard, an increased proportion of defense-related genes were upregulated in Tifguard than in the susceptible cultivar. Examples included disease resistance (R) proteins, leucine-rich repeats, stilbene synthase, dicer, and calmodulin. Pathway analysis revealed the increased downregulation of genes associated with defense and photosynthesis in the susceptible cultivar rather than in the resistant cultivar. These results suggest that essential physiological functions were less perturbed in the resistant cultivar than in the susceptible cultivar and that the defense response following TSWV infection was more robust in the resistant cultivar than in the susceptible cultivar.
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de Blas FJ, Bruno CI, Arias RS, Ballén-Taborda C, Mamani E, Oddino C, Rosso M, Costero BP, Bressano M, Soave JH, Soave SJ, Buteler MI, Seijo JG, Massa AN. Genetic mapping and QTL analysis for peanut smut resistance. BMC PLANT BIOLOGY 2021; 21:312. [PMID: 34215182 PMCID: PMC8252251 DOI: 10.1186/s12870-021-03023-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. batizocoi (K 9484)4×} segregating for the trait. RESULTS A SNP based genetic map arranged into 21 linkage groups belonging to the 20 peanut chromosomes was constructed with 1819 markers, spanning a genetic distance of 2531.81 cM. Two consistent quantitative trait loci (QTLs) were identified qSmIA08 and qSmIA02/B02, located on chromosome A08 and A02/B02, respectively. The QTL qSmIA08 at 15.20 cM/5.03 Mbp explained 17.53% of the phenotypic variance, while qSmIA02/B02 at 4.0 cM/3.56 Mbp explained 9.06% of the phenotypic variance. The combined genotypic effects of both QTLs reduced smut incidence by 57% and were stable over the 3 years of evaluation. The genome regions containing the QTLs are rich in genes encoding proteins involved in plant defense, providing new insights into the genetic architecture of peanut smut resistance. CONCLUSIONS A major QTL and a minor QTL identified in this study provide new insights into the genetic architecture of peanut smut resistance that may aid in breeding new varieties resistant to peanut smut.
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Affiliation(s)
- Francisco J de Blas
- Instituto Multidisciplinario de Biología Vegetal Consejo Nacional de Investigaciones en Ciencia y Tecnología (CONICET) y Universidad Nacional de Córdoba (UNC), Av. Vélez Sarsfield 1666, X5016GCN, Córdoba, Argentina
- Genética, Facultad de Ciencias Agropecuarias - UNC, Av. Ing. Agr. Félix A. Marrone 735, CP5001, Córdoba, Argentina
| | - Cecilia I Bruno
- Estadística y Biometría, FCA - UNC, Córdoba, Argentina
- CONICET, Av. Ing. Agr. Félix A. Marrone 735, CP5001, Córdoba, Argentina
| | - Renee S Arias
- USDA-ARS-National Peanut Research Laboratory (NPRL), Dawson, GA, 39842, USA
| | - Carolina Ballén-Taborda
- Center for Applied Genetic Technologies and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Eva Mamani
- Instituto Nacional Tecnología Agropecuaria (INTA), Ruta Nac. nro. 9 km 636 Estación Experimental Agropecuaria Manfredi, EEA, X5988 Manfredi, Córdoba, Argentina
| | - Claudio Oddino
- Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto (FAV-UNRC), Ruta Nacional 36, X5804BYA, Córdoba, Argentina
- Criadero El Carmen, Bv. Italia 835, CP5809, Gral. Cabrera, Córdoba, Argentina
| | - Melina Rosso
- Criadero El Carmen, Bv. Italia 835, CP5809, Gral. Cabrera, Córdoba, Argentina
| | - Beatriz P Costero
- Genética, Facultad de Ciencias Agropecuarias - UNC, Av. Ing. Agr. Félix A. Marrone 735, CP5001, Córdoba, Argentina
| | - Marina Bressano
- Biología Celular, FCA - UNC, Av. Ing. Agr. Félix A. Marrone 735, CP5001, Córdoba, Argentina
| | - Juan H Soave
- Criadero El Carmen, Bv. Italia 835, CP5809, Gral. Cabrera, Córdoba, Argentina
| | - Sara J Soave
- Criadero El Carmen, Bv. Italia 835, CP5809, Gral. Cabrera, Córdoba, Argentina
| | - Mario I Buteler
- Criadero El Carmen, Bv. Italia 835, CP5809, Gral. Cabrera, Córdoba, Argentina
| | - J Guillermo Seijo
- Instituto de Botánica del Nordeste (CONICET-UNNE) and Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina.
| | - Alicia N Massa
- USDA-ARS-National Peanut Research Laboratory (NPRL), Dawson, GA, 39842, USA.
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10
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Sinha P, Bajaj P, Pazhamala LT, Nayak SN, Pandey MK, Chitikineni A, Huai D, Khan AW, Desai A, Jiang H, Zhuang W, Guo B, Liao B, Varshney RK. Arachis hypogaea gene expression atlas for fastigiata subspecies of cultivated groundnut to accelerate functional and translational genomics applications. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2187-2200. [PMID: 32167667 PMCID: PMC7589347 DOI: 10.1111/pbi.13374] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 02/26/2020] [Indexed: 05/05/2023]
Abstract
Spatio-temporal and developmental stage-specific transcriptome analysis plays a crucial role in systems biology-based improvement of any species. In this context, we report here the Arachis hypogaea gene expression atlas (AhGEA) for the world's widest cultivated subsp. fastigiata based on RNA-seq data using 20 diverse tissues across five key developmental stages. Approximately 480 million paired-end filtered reads were generated followed by identification of 81 901 transcripts from an early-maturing, high-yielding, drought-tolerant groundnut variety, ICGV 91114. Further, 57 344 genome-wide transcripts were identified with ≥1 FPKM across different tissues and stages. Our in-depth analysis of the global transcriptome sheds light into complex regulatory networks namely gravitropism and photomorphogenesis, seed development, allergens and oil biosynthesis in groundnut. Importantly, interesting insights into molecular basis of seed development and nodulation have immense potential for translational genomics research. We have also identified a set of stable expressing transcripts across the selected tissues, which could be utilized as internal controls in groundnut functional genomics studies. The AhGEA revealed potential transcripts associated with allergens, which upon appropriate validation could be deployed in the coming years to develop consumer-friendly groundnut varieties. Taken together, the AhGEA touches upon various important and key features of cultivated groundnut and provides a reference for further functional, comparative and translational genomics research for various economically important traits.
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Affiliation(s)
- Pallavi Sinha
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Lekha T. Pazhamala
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Spurthi N. Nayak
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of BiotechnologyUniversity of Agricultural Sciences (UAS)DharwadIndia
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Dongxin Huai
- Oil Crop Research Institute (OCRI)Chinese Academy of Agricultural Science (CAAS)WuhanChina
| | - Aamir W. Khan
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aarthi Desai
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Huifang Jiang
- Oil Crop Research Institute (OCRI)Chinese Academy of Agricultural Science (CAAS)WuhanChina
| | - Weijian Zhuang
- College of Plant ProtectionFujian Agriculture and Forestry University (FAFU)FuzhouChina
| | - Baozhu Guo
- USDA‐ARS Crop Protection and Management Research Unit (CPMRU)TiftonGAUSA
| | - Boshou Liao
- Oil Crop Research Institute (OCRI)Chinese Academy of Agricultural Science (CAAS)WuhanChina
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
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11
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Wang X, Xu P, Ren Y, Yin L, Li S, Wang Y, Shi Y, Li H, Cao X, Chi X, Yu T, Pandey MK, Varshney RK, Yuan M. Genome-wide identification of meiotic recombination hot spots detected by SLAF in peanut (Arachis hypogaea L.). Sci Rep 2020; 10:13792. [PMID: 32796889 PMCID: PMC7429841 DOI: 10.1038/s41598-020-70354-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/14/2020] [Indexed: 11/10/2022] Open
Abstract
Recombination hot spots (RHP), caused by meiosis, are considered to play crucial roles in improvement and domestication of crop. Cultivated peanut is one of the most important rich-source of oil and protein crops. However, no direct scale of recombination events and RHP have been estimated for peanut. To examine the scale of recombination events and RHP in peanut, a RIL population with 200 lines and a natural population with 49 cultivars were evaluated. The precise integrated map comprises 4837 SLAF markers with genetic length of 2915.46 cM and density of 1.66 markers per cM in whole genome. An average of 30.0 crossover (2.06 cMMb−1) events was detected per RIL plant. The crossover events (CE) showed uneven distribution among B sub-genome (2.32) and A sub-genome (1.85). There were 4.34% and 7.86% of the genome contained large numbers of CE (> 50 cMMb−1) along chromosomes in F6 and natural population, respectively. High density of CE regions called RHP, showed negative relationship to marker haplotypes conservative region but positive to heatmap of recombination. The genes located within the RHP regions by GO categories showed the responding of environmental stimuli, which suggested that recombination plays a crucial role in peanut adaptation to changing environments
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Affiliation(s)
- Xiaohua Wang
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Ping Xu
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China.
| | - Yan Ren
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Liang Yin
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Shuangling Li
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Yan Wang
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Yanmao Shi
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Hui Li
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Xue Cao
- College of Agriculture and Forestry Science, Linyi University, Middle of Shuangling Road, Lanshan District, Linyi, 276000, China
| | - Xiaoyuan Chi
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Tianyi Yu
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China
| | - Manish K Pandey
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Patancheru, 502 324, India
| | - Rajeev K Varshney
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Greater Hyderabad, Patancheru, 502 324, India
| | - Mei Yuan
- Key Laboratory of Peanut Biology and Genetic Improvement, Ministry of Agriculture, Shandong Peanut Research Institute, No.126, Wannianquan Road, Licang District, Qingdao, 266100, China.
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12
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Zhang H, Chu Y, Dang P, Tang Y, Jiang T, Clevenger JP, Ozias-Akins P, Holbrook C, Wang ML, Campbell H, Hagan A, Chen C. Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2051-2061. [PMID: 32144466 DOI: 10.1007/s00122-020-03576-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
Two QTLs on ChrB09 significantly associated with both early and late leaf spots were identified by genome-wide association study in the US peanut mini-core collection. Early leaf spot (ELS) and late leaf spot (LLS) are two serious peanut diseases in the USA, causing tens of millions of dollars of annual economic losses. However, the genetic factors underlying resistance to those diseases in peanuts have not been well-studied. We conducted a genome-wide association study for the two peanut diseases using Affymetrix version 2.0 SNP array with 120 genotypes mainly coming from the US peanut mini-core collection. A total of 46 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.19 to 24.11%, in which eighteen QTLs are for resistance to ELS and 28 QTLs for LLS. Among the 46 QTLs, there were four and two major QTLs with PVE higher than 16.99% for resistance ELS and LLS, respectively. Of the six major QTLs, five were located on the B sub-genome and only one was on the A sub-genome, which suggested that the B sub-genome has more potential resistance genomic regions than the A sub-genome. In addition, two genomic regions on chromosome B09 were found to provide significant resistance to both ELS and LLS. A total of 74 non-redundant genes were identified as resistance genes, among which, twelve candidate genes were in significant genomic regions including two candidate genes for both ELS and LLS, and other ten candidate genes for ELS. The QTLs and candidate genes obtained from this study will be useful to breed peanuts for resistances to the diseases.
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Affiliation(s)
- Hui Zhang
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ye Chu
- Center for Applied Genetic Technologies, University of Georgia, Tifton, GA, 31793, USA
| | - Phat Dang
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, 39842, USA
| | - Yueyi Tang
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Tao Jiang
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Josh Paul Clevenger
- Center for Applied Genetic Technologies, University of Georgia, Tifton, GA, 31793, USA
| | - Peggy Ozias-Akins
- Center for Applied Genetic Technologies, University of Georgia, Tifton, GA, 31793, USA
| | - Corley Holbrook
- USDA-ARS Crop Genetics and Breeding Research, Tifton, GA, 31793, USA
| | - Ming Li Wang
- USDA-ARS Plant Genetic Resources Conservation, Griffin, GA, 30223, USA
| | - Howard Campbell
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Austin Hagan
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Charles Chen
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA.
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13
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Zhao Y, Ma J, Li M, Deng L, Li G, Xia H, Zhao S, Hou L, Li P, Ma C, Yuan M, Ren L, Gu J, Guo B, Zhao C, Wang X. Whole-genome resequencing-based QTL-seq identified AhTc1 gene encoding a R2R3-MYB transcription factor controlling peanut purple testa colour. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:96-105. [PMID: 31131506 PMCID: PMC6920131 DOI: 10.1111/pbi.13175] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/08/2023]
Abstract
Peanut (Arachis hypogaea. L) is an important oil crop worldwide. The common testa colours of peanut varieties are pink or red. But the peanut varieties with dark purple testa have been focused in recent years due to the potential high levels of anthocyanin, an added nutritional value of antioxidant. However, the genetic mechanism regulating testa colour of peanut is unknown. In this study, we found that the purple testa was decided by the female parent and controlled by a single major gene named AhTc1. To identify the candidate gene controlling peanut purple testa, whole-genome resequencing-based approach (QTL-seq) was applied, and a total of 260.9 Gb of data were generated from the parental and bulked lines. SNP index analysis indicated that AhTc1 located in a 4.7 Mb region in chromosome A10, which was confirmed by bulked segregant RNA sequencing (BSR) analysis in three segregation populations derived from the crosses between pink and purple testa varieties. Allele-specific markers were developed and demonstrated that the marker pTesta1089 was closely linked with purple testa. Further, AhTc1 encoding a R2R3-MYB gene was positional cloned. The expression of AhTc1 was significantly up-regulated in the purple testa parent YH29. Overexpression of AhTc1 in transgenic tobacco plants led to purple colour of leaves, flowers, pods and seeds. In conclusion, AhTc1, encoding a R2R3-MYB transcription factor and conferring peanut purple testa, was identified, which will be useful for peanut molecular breeding selection for cultivars with purple testa colour for potential increased nutritional value to consumers.
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Affiliation(s)
- Yuhan Zhao
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Junjie Ma
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong UniversityJinanChina
| | - Ming Li
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
| | - Li Deng
- Kaifeng Academy of Agriculture and ForestryKaifengChina
| | - Guanghui Li
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
| | - Han Xia
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Shuzhen Zhao
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Lei Hou
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
| | - Pengcheng Li
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Changle Ma
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Mei Yuan
- Shandong Peanut Research InstituteShandong, QingdaoChina
| | - Li Ren
- Kaifeng Academy of Agriculture and ForestryKaifengChina
| | - Jianzhong Gu
- Kaifeng Academy of Agriculture and ForestryKaifengChina
| | - Baozhu Guo
- Crop Protection and Management Research UnitUSDA‐Agricultural Research ServiceTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Chuanzhi Zhao
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
- Crop Protection and Management Research UnitUSDA‐Agricultural Research ServiceTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Xingjun Wang
- Biotechnology Research CenterShandong Academy of Agricultural SciencesShandong Provincial Key Laboratory of Crop Genetic ImprovementEcology and PhysiologyJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
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14
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Chaudhari S, Khare D, Patil SC, Sundravadana S, Variath MT, Sudini HK, Manohar SS, Bhat RS, Pasupuleti J. Genotype × Environment Studies on Resistance to Late Leaf Spot and Rust in Genomic Selection Training Population of Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2019; 10:1338. [PMID: 31867023 PMCID: PMC6904303 DOI: 10.3389/fpls.2019.01338] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/25/2019] [Indexed: 05/25/2023]
Abstract
Foliar fungal diseases especially late leaf spot (LLS) and rust are the important production constraints across the peanut growing regions of the world. A set of 340 diverse peanut genotypes that includes accessions from gene bank of International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), elite breeding lines from the breeding program, and popular cultivars were screened for LLS and rust resistance and yield traits across three locations in India under natural and artificial disease epiphytotic conditions. The study revealed significant variation among the genotypes for LLS and rust resistance at different environments. Combined analysis of variance revealed significant environment (E) and genotype × environment (G×E) interactions for both the diseases indicating differential response of genotypes in different environments. The present study reported 31 genotypes as resistant to LLS and 66 to rust across the locations at 90 DAS with maturity duration 103 to 128 days. Twenty-eight genotypes showed resistance to both the diseases across the locations, of which 19 derived from A. cardenasii, five from A. hypogaea, and four from A. villosa. Site regression and Genotype by Genotype x Environment (GGE) biplot analysis identified eight genotypes as stable for LLS, 24 for rust and 14 for pod yield under disease pressure across the environments. Best performing environment specific genotypes were also identified. Nine genotypes resistant to LLS and rust showed 77% to 120% increase in pod yield over control under disease pressure with acceptable pod and kernel features that can be used as potential parents in LLS and rust resistance breeding. Pod yield increase as a consequence of resistance offered to foliar fungal diseases suggests the possibility of considering 'foliar fungal disease resistance' as a must-have trait in all the peanut cultivars that will be released for cultivation in rainfed ecologies in Asia and Africa. The phenotypic data of the present study will be used for designing genomic selection prediction models in peanut.
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Affiliation(s)
- Sunil Chaudhari
- Crop Improvement- Asia Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Dhirendra Khare
- Department of Plant Breeding and Genetics, Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, India
| | - Sudam C. Patil
- Oilseeds Research Station, Mahatma Phule Krishi Vidyapeeth (MPKV), Jalgaon, India
| | | | - Murali T. Variath
- Crop Improvement- Asia Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Hari K. Sudini
- Crop Improvement- Asia Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surendra S. Manohar
- Crop Improvement- Asia Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramesh S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Janila Pasupuleti
- Crop Improvement- Asia Program, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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15
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A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea). Sci Rep 2019; 9:18246. [PMID: 31796847 PMCID: PMC6890646 DOI: 10.1038/s41598-019-54747-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/17/2019] [Indexed: 11/16/2022] Open
Abstract
Tomato spotted wilt virus (TSWV) is a devastating disease to peanut growers in the South-eastern region of the United States. Newly released peanut cultivars in recent years are crucial as they have some levels of resistance to TSWV. One mapping population of recombinant inbred line (RIL) used in this study was derived from peanut lines of SunOleic 97R and NC94022. A whole genome re-sequencing approach was used to sequence these two parents and 140 RILs. A recombination bin-based genetic map was constructed, with 5,816 bins and 20 linkage groups covering a total length of 2004 cM. Using this map, we identified three QTLs which were colocalized on chromosome A01. One QTL had the largest effect of 36.51% to the phenotypic variation and encompassed 89.5 Kb genomic region. This genome region had a cluster of genes, which code for chitinases, strictosidine synthase-like, and NBS-LRR proteins. SNPs linked to this QTL were used to develop Kompetitive allele specific PCR (KASP) markers, and the validated KASP markers showed expected segregation of alleles coming from resistant and susceptible parents within the population. Therefore, this bin-map and QTL associated with TSWV resistance made it possible for functional gene mapping, map-based cloning, and marker-assisted breeding. This study identified the highest number of SNP makers and demonstrated recombination bin-based map for QTL identification in peanut. The chitinase gene clusters and NBS-LRR disease resistance genes in this region suggest the possible involvement in peanut resistance to TSWV.
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16
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Lu Q, Hong Y, Li S, Liu H, Li H, Zhang J, Lan H, Liu H, Li X, Wen S, Zhou G, Varshney RK, Jiang H, Chen X, Liang X. Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.). BMC Genomics 2019; 20:799. [PMID: 31675924 PMCID: PMC6824139 DOI: 10.1186/s12864-019-6148-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 09/29/2019] [Indexed: 12/03/2022] Open
Abstract
Background Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. Results A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. Conclusions The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.
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Affiliation(s)
- Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Shaoxiong Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Jianan Zhang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang, China
| | - Haofa Lan
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang, China
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xingyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Shijie Wen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Guiyuan Zhou
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China.
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory for Crop Genetic Improvement, Guangzhou, 510640, China.
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17
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Desmae H, Janila P, Okori P, Pandey MK, Motagi BN, Monyo E, Mponda O, Okello D, Sako D, Echeckwu C, Oteng‐Frimpong R, Miningou A, Ojiewo C, Varshney RK. Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.). PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:425-444. [PMID: 31598026 PMCID: PMC6774334 DOI: 10.1111/pbr.12645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/04/2023]
Abstract
Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
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Affiliation(s)
- Haile Desmae
- International Crop Research Institute for the Semi‐Arid Tropics (ICRISAT)BamakoMali
| | | | | | | | | | | | - Omari Mponda
- Division of Research and Development (DRD)Tanzania Agricultural Research Institute (TARI) ‐ NaliendeleMtwaraTanzania
| | - David Okello
- National Agricultural Research Organization (NARO)EntebbeUganda
| | | | | | | | - Amos Miningou
- Institut National d'Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
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18
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Song H, Sun J, Yang G. The characteristic of Arachis duranensis-specific genes and their potential function. Gene 2019; 705:60-66. [PMID: 31009681 DOI: 10.1016/j.gene.2019.04.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/12/2019] [Accepted: 04/18/2019] [Indexed: 11/17/2022]
Abstract
Arachis species produce flowers aerially, and then grow into the ground, where they develop into fruits; a feature that is unique to Arachis species. We hypothesized that Arachis species evolved genes specifically involved in the control of aerial flowers and the formation of underground fruits. Arachis duranensis is more resistant to biotic and abiotic stressors. Here, we compared different legume species and identified Arachis duranensis-specific genes. We analyzed gene expression patterns, base substitution patterns and sequence features between genes that are conserved across legume plants and A. duranensis-specific genes. Furthermore, we tested the role of A. duranensis-specific genes during seed development, response to nematode Meloidogyne arenaria infection and drought stress. We found that A. duranensis-specific genes had characteristics of young genes. The gene expression level and breadth were lower in the A. duranensis-specific genes compared to conserved genes. The A. duranensis-specific genes had higher codon usage bias than conserved genes, and the polypeptide length and GC content at the three codon sites were lower compared to conserved genes. Of the A. duranensis-specific genes, single-copy and duplicated genes had different features. The RNA-seq result showed A. duranensis-specific genes were involved in seed development, as well as response to nematode infection and drought stress. In addition, we detected asymmetric functions in A. duranensis-specific duplicated genes in response to nematode infection and drought stress.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China.
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China.
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19
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Chu Y, Chee P, Culbreath A, Isleib TG, Holbrook CC, Ozias-Akins P. Major QTLs for Resistance to Early and Late Leaf Spot Diseases Are Identified on Chromosomes 3 and 5 in Peanut ( Arachis hypogaea). FRONTIERS IN PLANT SCIENCE 2019; 10:883. [PMID: 31333711 PMCID: PMC6625158 DOI: 10.3389/fpls.2019.00883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 06/20/2019] [Indexed: 05/21/2023]
Abstract
Early and late leaf spots (LLSs) are the major foliar diseases of peanut responsible for severely decreased yield in the absence of intensive fungicide spray programs. Pyramiding host resistance to leaf spots in elite cultivars is a sustainable solution to mitigate the diseases. In order to determine the genetic control of leaf spot disease resistance in peanut, a recombinant inbred line population (Florida-07 × GP-NC WS16) segregating for resistance to both diseases was used to construct a SNP-based linkage map consisting of 855 loci. QTL mapping revealed three resistance QTLs for LLS qLLSA05 (phenotypic variation explained, PVE = 7-10%), qLLSB03 (PVE = 5-7%), and qLLSB05 (PVE = 15-41%) that were consistently expressed over multi-year analysis. Two QTL, qLLSA05 and qLLSB05, confirmed our previously published QTL-seq results. For early leaf spot, three resistance QTLs were identified in multiple years, two on chromosome A03 (PVE = 8-12%) and one on chromosome B03 (PVE = 13-20%), with the locus qELSA03_1.1 coinciding with the previously published genomic region for LLS resistance in GPBD4. Comparative analysis of the genomic regions spanning the QTLs suggests that resistance to early and LLSs are largely genetically independent. In addition, QTL analysis on yield showed that the presence of resistance allele in qLLSB03 and qLLSB05 loci might result in protection from yield loss caused by LLS disease damage. Finally, post hoc analysis of the RIL subpopulation that was not utilized in the QTL mapping revealed that the flanking markers for these QTLs can successfully select for resistant and susceptible lines, confirming the effectiveness of pyramiding these resistance loci to improve host-plant resistance in peanut breeding programs using marker-assisted selection.
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Affiliation(s)
- Ye Chu
- Department of Horticulture, The University of Georgia Tifton Campus, Tifton, GA, United States
| | - Peng Chee
- Department of Crop and Soil Sciences, The University of Georgia Tifton Campus, Tifton, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, The University of Georgia Tifton Campus, Tifton, GA, United States
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Thomas G. Isleib
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - C. Corley Holbrook
- Institute of Plant Breeding, Genetics and Genomics, The University of Georgia Tifton Campus, Tifton, GA, United States
- United States Department of Agriculture (USDA), Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Peggy Ozias-Akins
- Department of Horticulture, The University of Georgia Tifton Campus, Tifton, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, The University of Georgia Tifton Campus, Tifton, GA, United States
- *Correspondence: Peggy Ozias-Akins,
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20
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Lu Q, Liu H, Hong Y, Li H, Liu H, Li X, Wen S, Zhou G, Li S, Chen X, Liang X. Consensus map integration and QTL meta-analysis narrowed a locus for yield traits to 0.7 cM and refined a region for late leaf spot resistance traits to 0.38 cM on linkage group A05 in peanut (Arachis hypogaea L.). BMC Genomics 2018; 19:887. [PMID: 30526476 PMCID: PMC6286586 DOI: 10.1186/s12864-018-5288-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/20/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many large-effect quantitative trait loci (QTLs) for yield and disease resistance related traits have been identified in different mapping populations of peanut (Arachis hypogaea L.) under multiple environments. However, only a limited number of QTLs have been used in marker-assisted selection (MAS) because of unfavorable epistatic interactions between QTLs in different genetic backgrounds. Thus, it is essential to identify consensus QTLs across different environments and genetic backgrounds for use in MAS. Here, we used QTL meta-analysis to identify a set of consensus QTLs for yield and disease resistance related traits in peanut. RESULTS A new integrated consensus genetic map with 5874 loci was constructed. The map comprised 20 linkage groups (LGs) and was up to a total length of 2918.62 cM with average marker density of 2.01 loci per centimorgan (cM). A total of 292 initial QTLs were projected on the new consensus map, and 40 meta-QTLs (MQTLs) for yield and disease resistance related traits were detected on four LGs. The genetic intervals of these consensus MQTLs varied from 0.20 cM to 7.4 cM, which is narrower than the genetic intervals of the initial QTLs, meaning they may be suitable for use in MAS. Importantly, a region of the map that previously co-localized multiple major QTLs for pod traits was narrowed from 3.7 cM to 0.7 cM using an overlap region of four MQTLs for yield related traits on LG A05, which corresponds to a physical region of about 630.3 kb on the A05 pseudomolecule of peanut, including 38 annotated candidate genes (54 transcripts) related to catalytic activity and metabolic process. Additionally, one major MQTL for late leaf spot (LLS) was identified in a region of about 0.38 cM. BLAST searches identified 26 candidate genes (30 different transcripts) in this region, some of which were annotated as related to regulation of disease resistance in different plant species. CONCLUSIONS Combined with the high-density marker consensus map, all the detected MQTLs could be useful in MAS. The biological functions of the 64 candidate genes should be validated to unravel the molecular mechanisms of yield and disease resistance in peanut.
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Affiliation(s)
- Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xingyu Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Shijie Wen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Guiyuan Zhou
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Shaoxiong Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China.
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China.
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21
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Song H, Guo Z, Chen T, Sun J, Yang G. Genome-wide identification of LRR-containing sequences and the response of these sequences to nematode infection in Arachis duranensis. BMC PLANT BIOLOGY 2018; 18:279. [PMID: 30424729 PMCID: PMC6234637 DOI: 10.1186/s12870-018-1508-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/29/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Leucine-rich repeat (LRR)-containing genes are involved in responses to various diseases. Recently, RNA-seq data from A. duranensis after nematode (Meloidogyne arenaria) infection were released. However, the number of LRR-containing genes present in A. duranensis and the response of LRR-containing genes to nematode infection are poorly understood. RESULTS In this study, we found 509 amino acid sequences containing nine types of LRR domains in A. duranensis. The inferred phylogenetic relationships revealed that the nine types of LRR domains had two originations. The inferred selective pressure was mainly consistent with LRR domains undergoing purifying selection. Twenty-one LRR-containing genes were associated with possible resistance to nematode infection after 3, 6, and 9 days. Among them, Aradu.T5WNW, Aradu.JM17V, and Aradu.MKP1A were up-regulate at these three time points, while Aradu.QD5DS and Aradu.M0ENQ were up-regulated 6 and 9 days after nematode infection. The expression of the above mentioned five genes was significantly and negatively correlated with the number of LRR8 domain, indicating that fewer LRR8 domains are associated with the promotion of LRR-containing genes that resist nematode infection. Patterns of co-expression and cis-acting elements indicated that WRKY possibly regulate the responses of LRR-containing genes to nematode infection and that expansin genes may work together with LRR-containing genes in response to nematode infection. CONCLUSIONS We identified the number and type of LRR-containing genes in A. duranensis. The LRR-containing genes that were found appear to be involved in responses to nematode infection. The number of LRR8 domains was negatively correlated with expression after nematode infection. The WRKY transcription factor may regulate resistance to nematode infection based on LRR-containing genes. Our results could improve the understanding of resistance to nematodes and molecular breeding in peanuts.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, 100871 China
| | - Tao Chen
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000 China
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
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22
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Agarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang G, Wang X, Deshmukh R, Holbrook CC, Bertioli DJ, Ozias‐Akins P, Jackson SA, Varshney RK, Guo B. High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1954-1967. [PMID: 29637729 PMCID: PMC6181220 DOI: 10.1111/pbi.12930] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/28/2018] [Accepted: 03/25/2018] [Indexed: 05/04/2023]
Abstract
Whole-genome resequencing (WGRS) of mapping populations has facilitated development of high-density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP-based high-density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence-based high-density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the 'T' population (Tifrunner × GT-C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high-density genetic map and multiple season phenotyping data identified 35 main-effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major-effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R-genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics-assisted breeding in peanut.
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Affiliation(s)
- Gaurav Agarwal
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Josh Clevenger
- Center for Applied Genetic TechnologiesMars Wrigley ConfectioneryAthensGAUSA
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Hui Wang
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Yaduru Shasidhar
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding & GenomicsUniversity of GeorgiaTiftonGAUSA
| | - Jake C. Fountain
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Divya Choudhary
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | | | | | | | - Xingjun Wang
- Shandong Academy of Agricultural SciencesBiotechnology Research CenterJinanChina
| | | | | | - David J. Bertioli
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Peggy Ozias‐Akins
- Department of Horticulture and Institute of Plant Breeding & GenomicsUniversity of GeorgiaTiftonGAUSA
| | - Scott A. Jackson
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Baozhu Guo
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
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23
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Han S, Yuan M, Clevenger JP, Li C, Hagan A, Zhang X, Chen C, He G. A SNP-Based Linkage Map Revealed QTLs for Resistance to Early and Late Leaf Spot Diseases in Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1012. [PMID: 30042783 PMCID: PMC6048419 DOI: 10.3389/fpls.2018.01012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/21/2018] [Indexed: 05/20/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important oilseed crop that is grown extensively in Africa, Asia and America. The diseases early and late leaf spot severely constrains peanut production worldwide. Because multiple genes control resistance to leaf spot diseases, conventional breeding is a time-consuming approach for pyramiding resistance genes into a single genotype. Marker-assisted selection (MAS) would complement and accelerate conventional breeding once molecular markers tightly associated with the resistance genes are identified. In this study, we have generated a large number of SNPs through genotyping by sequencing (GBS) and constructed a high-resolution map with an average distance of 1.34 cM among 2,753 SNP markers distributed on 20 linkage groups. QTL mapping has revealed that major QTL within a confidence interval could provide an efficient way to detect putative resistance genes. Analysis of the interval sequences has indicated that a major QTL for resistance to late leaf spot anchored by two NBS-LRR resistance genes on chromosome B05. Two major QTLs located on chromosomes A03 and B04 were associated with resistance genes for early leaf spot. Sequences within the confidence interval would facilitate identifying resistance genes and applying marker-assisted selection for resistance.
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Affiliation(s)
- Suoyi Han
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, United States
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Mei Yuan
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, United States
- Shandong Peanut Research Institute, Qingdao, China
| | - Josh P. Clevenger
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Chun Li
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Austin Hagan
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Xinyou Zhang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Charles Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Guohao He
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL, United States
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24
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Zhao Z, Tseng YC, Peng Z, Lopez Y, Chen CY, Tillman BL, Dang P, Wang J. Refining a major QTL controlling spotted wilt disease resistance in cultivated peanut (Arachis hypogaea L.) and evaluating its contribution to the resistance variations in peanut germplasm. BMC Genet 2018; 19:17. [PMID: 29571286 PMCID: PMC5865372 DOI: 10.1186/s12863-018-0601-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spotted wilt, caused by tomato spotted wilt virus (TSWV), has been one of major diseases in cultivated peanut grown in the southeastern United States (US) since 1990. Previously a major quantitative trait locus (QTL) controlling spotted wilt disease resistance was mapped to an interval of 2.55 cM genetic distance corresponding to a physical distance of 14.4 Mb on chromosome A01 of peanut by using a segregating F2 population. The current study focuses on refining this major QTL region and evaluating its contributions in the US peanut mini-core germplasm. RESULTS Two simple sequence repeat (SSR) markers associated with the major QTL were used to genotype F5 individuals, and 25 heterozygous individuals were selected and developed into an F6 segregating population. Based on visual evaluation in the field, a total of 194 susceptible F6 individuals were selected and planted into F7 generation for phenotyping. Nine SSR markers were used to genotype the 194 F6 individuals, and QTL analysis revealed that a confidence interval of 15.2 Mb region had the QTL with 22.8% phenotypic variation explained (PVE). This QTL interval was further genotyped using the Amplicon-seq method. A total of 81 non-redundant single nucleotide polymorphism (SNP) and eight InDel markers were detected. No recombinant was detected among the F6 individuals. Two InDel markers were integrated into the linkage group and helped to refine the confidence interval of this QTL into a 0.8 Mb region. To test the QTL contributes to the resistance variance in US peanut mini-core germplasm, two flanking SSR markers were used to genotype 107 mini-core germplasm accessions. No statistically significant association was observed between the genotype at the QTL region and spotted wilt resistance in the mini-core germplasm, which indicated that the resistance allelic region at this QTL didn't contribute to the resistance variance in the US peanut mini-core germplasm, thus was a unique resistance source. CONCLUSION A major QTL related to spotted wilt disease resistance in peanut was refined to a 0.8 Mb region on A01 chromosome, which didn't relate to spotted wilt disease resistance in the US peanut mini-core germplasm and might be a unique genetic source.
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Affiliation(s)
- Zifan Zhao
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Yu-Chien Tseng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.,North Florida Research and Education Center, University of Florida, Marianna, FL, 32446, USA
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Yolanda Lopez
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Barry L Tillman
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.,North Florida Research and Education Center, University of Florida, Marianna, FL, 32446, USA
| | - Phat Dang
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, 39842, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA. .,Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
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25
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Classical and Molecular Approaches for Mapping of Genes and Quantitative Trait Loci in Peanut. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-63935-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
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26
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Song H, Gao H, Liu J, Tian P, Nan Z. Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs. Sci Rep 2017; 7:14853. [PMID: 29093502 PMCID: PMC5665869 DOI: 10.1038/s41598-017-13981-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/04/2017] [Indexed: 11/22/2022] Open
Abstract
The relationship between evolutionary rates and gene expression in model plant orthologs is well documented. However, little is known about the relationships between gene expression and evolutionary trends in Arachis orthologs. We identified 7,435 one-to-one orthologs, including 925 single-copy and 6,510 multiple-copy sequences in Arachis duranensis and Arachis ipaënsis. Codon usage was stronger for shorter polypeptides, which were encoded by codons with higher GC contents. Highly expressed coding sequences had higher codon usage bias, GC content, and expression breadth. Additionally, expression breadth was positively correlated with polypeptide length, but there was no correlation between gene expression and polypeptide length. Inferred selective pressure was also negatively correlated with both gene expression and expression breadth in all one-to-one orthologs, while positively but non-significantly correlated with gene expression in sequences with signatures of positive selection. Gene expression levels and expression breadth were significantly higher for single-copy genes than for multiple-copy genes. Similarly, the gene expression and expression breadth in sequences with signatures of purifying selection were higher than those of sequences with positive selective signatures. These results indicated that gene expression differed between single-copy and multiple-copy genes as well as sequences with signatures of positive and purifying selection.
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Affiliation(s)
- Hui Song
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
| | - Hongjuan Gao
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Jing Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Pei Tian
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
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Zhang X, Zhang J, He X, Wang Y, Ma X, Yin D. Genome-Wide Association Study of Major Agronomic Traits Related to Domestication in Peanut. FRONTIERS IN PLANT SCIENCE 2017; 8:1611. [PMID: 29018458 PMCID: PMC5623184 DOI: 10.3389/fpls.2017.01611] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/04/2017] [Indexed: 05/04/2023]
Abstract
Peanut (Arachis hypogaea) consists of two subspecies, hypogaea and fastigiata, and has been cultivated worldwide for hundreds of years. Here, 158 peanut accessions were selected to dissect the molecular footprint of agronomic traits related to domestication using specific-locus amplified fragment sequencing (SLAF-seq method). Then, a total of 17,338 high-quality single nucleotide polymorphisms (SNPs) in the whole peanut genome were revealed. Eleven agronomic traits in 158 peanut accessions were subsequently analyzed using genome-wide association studies (GWAS). Candidate genes responsible for corresponding traits were then analyzed in genomic regions surrounding the peak SNPs, and 1,429 genes were found within 200 kb windows centerd on GWAS-identified peak SNPs related to domestication. Highly differentiated genomic regions were observed between hypogaea and fastigiata accessions using FST values and sequence diversity (π) ratios. Among the 1,429 genes, 662 were located on chromosome A3, suggesting the presence of major selective sweeps caused by artificial selection during long domestication. These findings provide a promising insight into the complicated genetic architecture of domestication-related traits in peanut, and reveal whole-genome SNP markers of beneficial candidate genes for marker-assisted selection (MAS) in future breeding programs.
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