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Chen H, Liu N, Huang L, Huai D, Xu R, Chen X, Guo S, Chen J, Jiang H. Identification of a Major QTL for Seed Protein Content in Cultivated Peanut ( Arachis hypogaea L.) Using QTL-Seq. PLANTS (BASEL, SWITZERLAND) 2024; 13:2368. [PMID: 39273852 PMCID: PMC11396936 DOI: 10.3390/plants13172368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/28/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024]
Abstract
Peanut (Arachis hypogaea L.) is a great plant protein source for human diet since it has high protein content in the kernel. Therefore, seed protein content (SPC) is considered a major agronomic and quality trait in peanut breeding. However, few genetic loci underlying SPC have been identified in peanuts, and the underlying regulatory mechanisms remain unknown, limiting the effectiveness of breeding for high-SPC peanut varieties. In this study, a major QTL (qSPCB10.1) controlling peanut SPC was identified within a 2.3 Mb interval in chromosome B10 by QTL-seq using a recombinant inbred line population derived from parental lines with high and low SPCs, respectively. Sequence comparison, transcriptomic analysis, and annotation analysis of the qSPCB10.1 locus were performed. Six differentially expressed genes with sequence variations between two parents were identified as candidate genes underlying qSPCB10.1. Further locus interaction analysis revealed that qSPCB10.1 could not affect the seed oil accumulation unless qOCA08.1XH13 was present, a high seed oil content (SOC) allele for a major QTL underlying SOC. In summary, our study provides a basis for future investigation of the genetic basis of seed protein accumulation and facilitates marker-assisted selection for developing high-SPC peanut genotypes.
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Affiliation(s)
- Hao Chen
- Institute of Crop Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People's Republic of China, Wuhan 430062, China
| | - Nian Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People's Republic of China, Wuhan 430062, China
| | - Li Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People's Republic of China, Wuhan 430062, China
| | - Dongxin Huai
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People's Republic of China, Wuhan 430062, China
| | - Rirong Xu
- Institute of Crop Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Xiangyu Chen
- Institute of Crop Sciences, Fujian Research Station of Crop Gene Resource & Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People's Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Shengyao Guo
- Quanzhou Institute of Agricultural Sciences, Jinjiang 362212, China
| | - Jianhong Chen
- Quanzhou Institute of Agricultural Sciences, Jinjiang 362212, China
| | - Huifang Jiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People's Republic of China, Wuhan 430062, China
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Mangal V, Verma LK, Singh SK, Saxena K, Roy A, Karn A, Rohit R, Kashyap S, Bhatt A, Sood S. Triumphs of genomic-assisted breeding in crop improvement. Heliyon 2024; 10:e35513. [PMID: 39170454 PMCID: PMC11336775 DOI: 10.1016/j.heliyon.2024.e35513] [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: 03/03/2024] [Revised: 07/23/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Conventional breeding approaches have played a significant role in meeting the food demand remarkably well until now. However, the increasing population, yield plateaus in certain crops, and limited recombination necessitate using genomic resources for genomics-assisted crop improvement programs. As a result of advancements in the next-generation sequence technology, GABs have developed dramatically to characterize allelic variants and facilitate their rapid and efficient incorporation in crop improvement programs. Genomics-assisted breeding (GAB) has played an important role in harnessing the potential of modern genomic tools, exploiting allelic variation from genetic resources and developing cultivars over the past decade. The availability of pangenomes for major crops has been a significant development, albeit with varying degrees of completeness. Even though adopting these technologies is essentially determined on economic grounds and cost-effective assays, which create a wealth of information that can be successfully used to exploit the latent potential of crops. GAB has been instrumental in harnessing the potential of modern genomic resources and exploiting allelic variation for genetic enhancement and cultivar development. GAB strategies will be indispensable for designing future crops and are expected to play a crucial role in breeding climate-smart crop cultivars with higher nutritional value.
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Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
| | | | - Sandeep Kumar Singh
- Department of Genetics and Plant Breeding, Faculty of Agricultural Sciences, Siksha ‘O’ Anusandhan University, Bhubaneswar, Odisha, 751030, India
| | - Kanak Saxena
- Department of Genetics and Plant Breeding, Rabindranath Tagore University, Raisen, Madhya Pradesh, India
| | - Anirban Roy
- Division of Genetics and Plant Breeding, Ramakrishna Mission Vivekananda Educational and Research Institute (RKMVERI), Narendrapur, Kolkata, 700103, India
| | - Anandi Karn
- Plant Breeding & Graduate Program, IFAS - University of Florida, Gainesville, USA
| | - Rohit Rohit
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Shruti Kashyap
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Ashish Bhatt
- Department of Genetics and Plant Breeding, GBPUA&T, Pantnagar, Uttarakhand, 263145, India
| | - Salej Sood
- ICAR-Central Potato Research Institute (CPRI), Shimla, Himachal Pradesh, 171001, India
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3
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Zhang H, Tang Y, Yue Y, Chen Y. Advances in the evolution research and genetic breeding of peanut. Gene 2024; 916:148425. [PMID: 38575102 DOI: 10.1016/j.gene.2024.148425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/15/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Peanut is an important cash crop used in oil, food and feed in our country. The rapid development of sequencing technology has promoted the research on the related aspects of peanut genetic breeding. This paper reviews the research progress of peanut origin and evolution, genetic breeding, molecular markers and their applications, genomics, QTL mapping and genome selection techniques. The main problems of molecular genetic breeding in peanut research worldwide include: the narrow genetic resources of cultivated species, unstable genetic transformation and unclear molecular mechanism of important agronomic traits. Considering the severe challenges regarding the supply of edible oil, and the main problems in peanut production, the urgent research directions of peanut are put forward: The de novo domestication and the exploitation of excellent genes from wild resources to improve modern cultivars; Integration of multi-omics data to enhance the importance of big data in peanut genetics and breeding; Cloning the important genes related to peanut agronomic traits and analyzing their fine regulation mechanisms; Precision molecular design breeding and using gene editing technology to accurately improve the key traits of peanut.
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Affiliation(s)
- Hui Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
| | - Yueyi Tang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Yunlai Yue
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yong Chen
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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4
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Wang F, Miao H, Zhang S, Hu X, Li C, Chu Y, Chen C, Zhong W, Zhang T, Wang H, Xu L, Yang W, Chen J. Identification of a major QTL underlying sugar content in peanut kernels based on the RIL mapping population. FRONTIERS IN PLANT SCIENCE 2024; 15:1423586. [PMID: 39027670 PMCID: PMC11254704 DOI: 10.3389/fpls.2024.1423586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024]
Abstract
High sugar content in peanut seeds is one of the major breeding objectives for peanut flavor improvement. In order to explore the genetic control of sugar accumulation in peanut kernels, we constructed a recombinant inbred line population of 256 F2:6-7 lines derived from the Luhua11 × 06B16 cross. A high-resolution genetic map was constructed with 3692 bin markers through whole genome re-sequencing. The total map distance was 981.65 cM and the average bin marker distance was 0.27cM. A major stable QTL region (qSCB09/qSSCB09) was identified on linkage group (LG) B09 associated with both sucrose content (SC) and soluble sugar content (SSC) explaining 21.51-33.58% phenotypic variations. This major QTL region was consistently detected in three environments and mapped within a physical interval of 1.56 Mb on chromosome B09, and six candidate genes were identified. These results provide valuable information for further map-based cloning of favorable allele for sugar content in peanut.
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Affiliation(s)
- Feifei Wang
- Shandong Peanut Research Institute, Qingdao, China
| | - Huarong Miao
- Shandong Peanut Research Institute, Qingdao, China
| | | | - Xiaohui Hu
- Shandong Peanut Research Institute, Qingdao, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Ye Chu
- Department of Horticulture, University of Georgia, Tifton, GA, United States
| | - Charles Chen
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Wen Zhong
- Shandong Seed Administration Station, Jinan, Shandong, China
| | - Tianyu Zhang
- Shandong Seed Administration Station, Jinan, Shandong, China
| | - Heng Wang
- Rizhao Agricultural Technical Service Center, Rizhao, Shandong, China
| | - Linying Xu
- Cixi Agricultural Science Research Institute, Cixi, Ningbo, Zhejiang, China
| | | | - Jing Chen
- Shandong Peanut Research Institute, Qingdao, China
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5
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Rani K, Gangadhara K, Ajay BC, Kona P, Kumar N, Bera SK. A comprehensive phenotypic and genotypic evaluation of Spanish groundnuts from diverse crosses to identify superior and stable donors for fresh seed dormancy. Sci Rep 2024; 14:14988. [PMID: 38951551 PMCID: PMC11217502 DOI: 10.1038/s41598-024-64681-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
Breeding high yielding groundnut cultivars with 2-3 weeks of fresh seed dormancy, particularly in Spanish-type cultivars, enhances the sustainability of agriculture in groundnuts. In this context, we conducted a comprehensive phenotypic and genotypic evaluation of advanced breeding lines developed in the genetic background of Spanish types. By employing multi-phenotyping and marker data, we identified PBS 15044, 16004, 16013, 16015, 16016, 16017, 16020, 16021, 16026, 16031, 16035, 16037, 16038, 16039, 16041, and 16042 with 2-3 weeks dormancy (> 90%).The various parametric and non-parametric estimates identified the stable fresh dormant genotypes with one or more superior economic trait. PBS 16021, 15044, 16038, and 16039 identified with high hundred pod weight (HPW) were also reported having high intensity of dormancy (> 90% for up to 3 weeks); PBS 15044, 16016, PBS 16038 and PBS 16039 with high hundred kernel weight (HKW) also reported with up to 3 weeks fresh seed dormancy; and PBS 16013, 16031, and 16038 with up to 3 weeks fresh seed dormancy had high shelling percentage (SP). They can be used to develop lines with the desired level of dormancy, and high yields, by designing appropriate breeding strategies.
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Affiliation(s)
- Kirti Rani
- ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, India.
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Jodhpur, Rajasthan, India.
| | - K Gangadhara
- ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, India
- ICAR-Central Tobacco Research Institute, Research Station Kandukur, Kandukur, Andhra Pradesh, India
| | - B C Ajay
- ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, India
| | - Praveen Kona
- ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, India
| | - Narendra Kumar
- ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, India
| | - S K Bera
- ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, India.
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6
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Lv Z, Lan G, Bai B, Yu P, Wang C, Zhang H, Zhong C, Zhao X, Yu H. Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq. Genomics 2024; 116:110835. [PMID: 38521201 DOI: 10.1016/j.ygeno.2024.110835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
Pod length (PL) is one of the major traits determining pod size and yield of peanut. Discovering the quantitative trait loci (QTL) and identifying candidate genes associated with PL are essential for breeding high-yield peanut. In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F2 population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265.93 kb region by traditional QTL approach. RNA-seq analysis showed that there were four differentially expressed genes (DEGs) in the candidate region, among which Arahy.PF2L6F (AhCDC48) and Arahy.P4LK2T (AhTAA1) were speculated to be PL-related candidate genes. These results were informative for the elucidation of the underlying regulatory mechanism in peanut pod length and would facilitate further identification of valuable target genes.
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Affiliation(s)
- Zhenghao Lv
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Guohu Lan
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Baiyi Bai
- College of Agriculture and Horticulture, Liaoning Agriculture Ovcational and Technical College, Yingkou 115009, China
| | - Penghao Yu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Chuantang Wang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Shandong Peanut Research Institute, Qingdao 266100, China
| | - He Zhang
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Chao Zhong
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinhua Zhao
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiqiu Yu
- Peanut Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; College of Agriculture and Horticulture, Liaoning Agriculture Ovcational and Technical College, Yingkou 115009, China.
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7
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Pandey MK, Gangurde SS, Shasidhar Y, Sharma V, Kale SM, Khan AW, Shah P, Joshi P, Bhat RS, Janila P, Bera SK, Varshney RK. High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut. BMC PLANT BIOLOGY 2024; 24:262. [PMID: 38594614 PMCID: PMC11005153 DOI: 10.1186/s12870-024-04987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Foliar diseases namely late leaf spot (LLS) and leaf rust (LR) reduce yield and deteriorate fodder quality in groundnut. Also the high oleic acid content has emerged as one of the most important traits for industries and consumers due to its increased shelf life and health benefits. RESULTS Genetic mapping combined with pooled sequencing approaches identified candidate resistance genes (LLSR1 and LLSR2 for LLS and LR1 for LR) for both foliar fungal diseases. The LLS-A02 locus housed LLSR1 gene for LLS resistance, while, LLS-A03 housed LLSR2 and LR1 genes for LLS and LR resistance, respectively. A total of 49 KASPs markers were developed from the genomic regions of important disease resistance genes, such as NBS-LRR, purple acid phosphatase, pentatricopeptide repeat-containing protein, and serine/threonine-protein phosphatase. Among the 49 KASP markers, 41 KASPs were validated successfully on a validation panel of contrasting germplasm and breeding lines. Of the 41 validated KASPs, 39 KASPs were designed for rust and LLS resistance, while two KASPs were developed using fatty acid desaturase (FAD) genes to control high oleic acid levels. These validated KASP markers have been extensively used by various groundnut breeding programs across the world which led to development of thousands of advanced breeding lines and few of them also released for commercial cultivation. CONCLUSION In this study, high-throughput and cost-effective KASP assays were developed, validated and successfully deployed to improve the resistance against foliar fungal diseases and oleic acid in groundnut. So far deployment of allele-specific and KASP diagnostic markers facilitated development and release of two rust- and LLS-resistant varieties and five high-oleic acid groundnut varieties in India. These validated markers provide opportunities for routine deployment in groundnut breeding programs.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pushpesh Joshi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip K Bera
- ICAR-Directorate of Groundnut Research, Junagadh, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia.
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8
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Lateef I, Katoch S, Katoch A, Badiyal A, Pathania A, Dhiman S, Nisa Q, Bashir A, Nabi A, Nabi N, Fayaz T, Gulzar G, Shah MD, Shikari AB, Dar ZA, Itoo H, Shah RA, Sofi TA, Sharma V, Sharma MK, Rathour R, Sharma PN, Padder BA. Fine mapping of a new common bean anthracnose resistance gene (Co-18) to the proximal end of Pv10 in Indian landrace KRC-5. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:32. [PMID: 38270625 DOI: 10.1007/s00122-023-04539-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024]
Abstract
KEY MESSAGE Mapping and fine mapping of bean anthracnose resistance genes is a continuous process. We report fine mapping of anthracnose resistance gene Co-18 which is the first anthracnose gene mapped to Pv10. The discovery of resistance gene is a major gain in the bean anthracnose pathosystem research. Among the Indian common bean landraces, KRC-5 exhibit high levels of resistance to the bean anthracnose pathogen Colletotrichum lindemuthianum. To precisely map the anthracnose resistance gene, we used a Recombinant Inbred Line (F2:9 RIL) population (KRC-5 × Jawala). The inheritance test revealed that KRC-5 carries a dominant resistance gene temporarily designated as Co-18. We discovered two RAPD markers linked to Co-18 among 287 RAPD markers. These RAPD markers were eventually developed into SCARs (Sc-OPR15 and Sc-OPF6) and flank Co-18 on chromosome Pv10 at a distance of 5.3 and 4.2 cM, respectively. At 4.0-4.1 Mb on Pv10, we detected a SNP (single-nucleotide polymorphism) signal. We synthesized 58 SSRs and 83 InDels from a pool of 135 SSRs and 1134 InDels, respectively. Five SSRs, four InDels, and two SCARs were used to generate the high-density linkage map, which led to the identification of two SSRs (SSR24 and SSR36) that are tightly linked to Co-18. These two SSRs flank the Co-18 to 178 kb genomic region with 13 candidate genes including five NLR (nucleotide-binding and leucine-rich repeat) genes. The closely linked markers SSR24 and SSR36 will be used in cloning and pyramiding of the Co-18 gene with other R genes to develop durable resistant bean varieties.
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Affiliation(s)
- Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Shabnam Katoch
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Abhishek Katoch
- University Institute of Agricultural Sciences, Chandigarh University, Ajitgarh, India
| | - Anila Badiyal
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Anju Pathania
- Faculty of Agriculture, DAV University, Jalandhar, Punjab, 144001, India
| | - Shiwali Dhiman
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Adfar Bashir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Naziya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Tabia Fayaz
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Gazala Gulzar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Mehraj D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Asif B Shikari
- Division of Plant Breeding and Genetics, SKUAST-K, FoA, Wadura, Baramulla, Sopore, India
| | | | - Hamidullah Itoo
- Ambri Apple Research Center, Pahanoo, SKUAST-K, Shopian, 192303, India
| | - Rafiq A Shah
- Ambri Apple Research Center, Pahanoo, SKUAST-K, Shopian, 192303, India
| | - Tariq A Sofi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Vivek Sharma
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - M K Sharma
- Division of Fruit Science, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - P N Sharma
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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9
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Ni J, You C, Chen Z, Tang D, Wu H, Deng W, Wang X, Yang J, Bao R, Liu Z, Meng P, Rong T, Liu J. Deploying QTL-seq rapid identification and separation of the major QTLs of tassel branch number for fine-mapping in advanced maize populations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:88. [PMID: 38045561 PMCID: PMC10686902 DOI: 10.1007/s11032-023-01431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023]
Abstract
The tassel competes with the ear for nutrients and shields the upper leaves, thereby reducing the yield of grain. The tassel branch number (TBN) is a pivotal determinant of tassel size, wherein the reduced TBN has the potential to enhance the transmission of light and reduce the consumption of nutrients, which should ultimately result in increased yield. Consequently, the TBN has emerged as a vital target trait in contemporary breeding programs that focus on compact maize varieties. In this study, QTL-seq technology and advanced population mapping were used to rapidly identify and dissect the major effects of the TBN on QTL. Advanced mapping populations (BC4F2 and BC4F3) were derived from the inbred lines 18-599 (8-11 TBN) and 3237 (0-1 TBN) through phenotypic recurrent selection. First, 13 genomic regions associated with the TBN were detected using quantitative trait locus (QTL)-seq and were located on chromosomes 2 and 5. Subsequently, validated loci within these regions were identified by QTL-seq. Three QTLs for TBN were identified in the BC4F2 populations by traditional QTL mapping, with each QTL explaining the phenotypic variation of 6.13-18.17%. In addition, for the major QTL (qTBN2-2 and qTBN5-1), residual heterozygous lines (RHLs) were developed from the BC4F2 population. These two major QTLs were verified in the RHLs by QTL mapping, with the phenotypic variation explained (PVE) of 21.57% and 30.75%, respectively. Near-isogenic lines (NILs) of qTBN2-2 and qTBN5-1 were constructed. There were significant differences between the NILs in TBN. These results will enhance our understanding of the genetic basis of TBN and provide a solid foundation for the fine-mapping of TBN. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01431-y.
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Affiliation(s)
- Jixing Ni
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Chong You
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Zhengjie Chen
- Sichuan Advanced Agricultural & Industrial Institute, China Agriculture University, No.8 Xingyuan Road, Xinjin District, Chengdu, 611430 Sichuan China
| | - Dengguo Tang
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Haimei Wu
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Wujiao Deng
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Xueying Wang
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Jinchang Yang
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Ruifan Bao
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Zhiqin Liu
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Pengxu Meng
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
| | - Jian Liu
- Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130 Sichuan China
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Parmar S, Janila P, Gangurde SS, Variath MT, Sharma V, Bomireddy D, Manohar SS, Varshney RK, Singam P, Pandey MK. Genetic mapping identified major main-effect and three co-localized quantitative trait loci controlling high iron and zinc content in groundnut. THE PLANT GENOME 2023; 16:e20361. [PMID: 37408143 DOI: 10.1002/tpg2.20361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.
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Affiliation(s)
- Sejal Parmar
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Pasupuleti Janila
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sunil S Gangurde
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Murali T Variath
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Deekshitha Bomireddy
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surendra S Manohar
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish K Pandey
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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11
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Gangurde SS, Khan AW, Janila P, Variath MT, Manohar SS, Singam P, Chitikineni A, Varshney RK, Pandey MK. Whole-genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut. THE PLANT GENOME 2023; 16:e20265. [PMID: 36478184 DOI: 10.1002/tpg2.20265] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/16/2022] [Indexed: 06/17/2023]
Abstract
Seed weight in groundnut (Arachis hypogaea L.) has direct impact on yield as well as market price because of preference for bold seeds by consumers and industry, thereby making seed-size improvement as one of the most important objectives of groundnut breeding programs globally. Marker-based early generation selection can accelerate the process of breeding for developing large-seeded varieties. In this context, we deployed the quantitative trait locus-sequencing (QTL-seq) approach on a biparental mapping population (Chico × ICGV 02251) to identify candidate genes and develop markers for seed weight in groundnut. A total of 289.4-389.4 million reads sequencing data were generated from three libraries (ICGV 02251 and two extreme bulks) achieving 93.9-95.1% genome coverage and 8.34-9.29× average read depth. The analysis of sequencing data using QTL-seq pipeline identified five genomic regions (three on chromosome B06 and one each on chromosomes B08 and B09) for seed weight. Detailed analysis of above associated genomic regions detected 182 single-nucleotide polymorphisms (SNPs) in genic and intergenic regions, and 11 of these SNPs were nonsynonymous in the genomic regions of 10 candidate genes including Ulp proteases and BIG SEED locus genes. Kompetitive allele specific polymerase chain reaction (KASP) markers for 14 SNPs were developed, and four of these markers (snpAH0031, snpAH0033, snpAH0037, and snpAH0038) were successfully validated for deployment in breeding for large-seeded groundnut varieties.
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Affiliation(s)
- Sunil S Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- Dep. of Genetics, Osmania Univ., Hyderabad, 500007, India
| | - Aamir W Khan
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pasupuleti Janila
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Murali T Variath
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Surendra S Manohar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch Univ., Murdoch, Western Australia, 6150, Australia
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
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Kitashova A, Brodsky V, Chaturvedi P, Pierides I, Ghatak A, Weckwerth W, Nägele T. Quantifying the impact of dynamic plant-environment interactions on metabolic regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 290:154116. [PMID: 37839392 DOI: 10.1016/j.jplph.2023.154116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.
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Affiliation(s)
- Anastasia Kitashova
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Vladimir Brodsky
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Palak Chaturvedi
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Iro Pierides
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Arindam Ghatak
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Wolfram Weckwerth
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Thomas Nägele
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
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13
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Yang H, Luo L, Li Y, Li H, Zhang X, Zhang K, Zhu S, Li X, Li Y, Wan Y, Liu F. Fine mapping of qAHPS07 and functional studies of AhRUVBL2 controlling pod size in peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1785-1798. [PMID: 37256840 PMCID: PMC10440995 DOI: 10.1111/pbi.14076] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 04/18/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important oil and cash crop. Pod size is one of the major traits determining yield and commodity characteristic of peanut. Fine mapping of quantitative trait locus (QTL) and identification of candidate genes associated with pod size are essential for genetic improvement and molecular breeding of peanut varieties. In this study, a major QTL related to pod size, qAHPS07, was fine mapped to a 36.46 kb interval on chromosome A07 using F2 , recombinant inbred line (RIL) and secondary F2 populations. qAHPS07 explained 38.6%, 23.35%, 37.48%, 25.94% of the phenotypic variation for single pod weight (SPW), pod length (PL), pod width (PW) and pod shell thickness (PST), respectively. Whole genome resequencing and gene expression analysis revealed that a RuvB-like 2 protein coding gene AhRUVBL2 was the most likely candidate for qAHPS07. Overexpression of AhRUVBL2 in Arabidopsis led to larger seeds and plants than the wild type. AhRUVBL2-silenced peanut seedlings represented small leaves and shorter main stems. Three haplotypes were identified according to three SNPs in the promoter of AhRUVBL2 among 119 peanut accessions. Among them, SPW, PW and PST of accessions carrying Hap_ATT represent 17.6%, 11.2% and 26.3% higher than those carrying Hap_GAC,respectively. In addition, a functional marker of AhRUVBL2 was developed. Taken together, our study identified a key functional gene of peanut pod size, which provides new insights into peanut pod size regulation mechanism and offers practicable markers for the genetic improvement of pod size-related traits in peanut breeding.
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Affiliation(s)
- Hui Yang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Lu Luo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yuying Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Huadong Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Xiurong Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Kun Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Suqing Zhu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Xuanlin Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yingjie Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
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14
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Chawla R, Poonia A, Samantara K, Mohapatra SR, Naik SB, Ashwath MN, Djalovic IG, Prasad PVV. Green revolution to genome revolution: driving better resilient crops against environmental instability. Front Genet 2023; 14:1204585. [PMID: 37719711 PMCID: PMC10500607 DOI: 10.3389/fgene.2023.1204585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/11/2023] [Indexed: 09/19/2023] Open
Abstract
Crop improvement programmes began with traditional breeding practices since the inception of agriculture. Farmers and plant breeders continue to use these strategies for crop improvement due to their broad application in modifying crop genetic compositions. Nonetheless, conventional breeding has significant downsides in regard to effort and time. Crop productivity seems to be hitting a plateau as a consequence of environmental issues and the scarcity of agricultural land. Therefore, continuous pursuit of advancement in crop improvement is essential. Recent technical innovations have resulted in a revolutionary shift in the pattern of breeding methods, leaning further towards molecular approaches. Among the promising approaches, marker-assisted selection, QTL mapping, omics-assisted breeding, genome-wide association studies and genome editing have lately gained prominence. Several governments have progressively relaxed their restrictions relating to genome editing. The present review highlights the evolutionary and revolutionary approaches that have been utilized for crop improvement in a bid to produce climate-resilient crops observing the consequence of climate change. Additionally, it will contribute to the comprehension of plant breeding succession so far. Investing in advanced sequencing technologies and bioinformatics will deepen our understanding of genetic variations and their functional implications, contributing to breakthroughs in crop improvement and biodiversity conservation.
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Affiliation(s)
- Rukoo Chawla
- Department of Genetics and Plant Breeding, Maharana Pratap University of Agriculture and Technology, Udaipur, Rajasthan, India
| | - Atman Poonia
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Bawal, Haryana, India
| | - Kajal Samantara
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Sourav Ranjan Mohapatra
- Department of Forest Biology and Tree Improvement, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - S. Balaji Naik
- Institute of Integrative Biology and Systems, University of Laval, Quebec City, QC, Canada
| | - M. N. Ashwath
- Department of Forest Biology and Tree Improvement, Kerala Agricultural University, Thrissur, Kerala, India
| | - Ivica G. Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Novi Sad, Serbia
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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15
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Kassie FC, Nguepjop JR, Ngalle HB, Assaha DVM, Gessese MK, Abtew WG, Tossim HA, Sambou A, Seye M, Rami JF, Fonceka D, Bell JM. An Overview of Mapping Quantitative Trait Loci in Peanut ( Arachis hypogaea L.). Genes (Basel) 2023; 14:1176. [PMID: 37372356 DOI: 10.3390/genes14061176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Quantitative Trait Loci (QTL) mapping has been thoroughly used in peanut genetics and breeding in spite of the narrow genetic diversity and the segmental tetraploid nature of the cultivated species. QTL mapping is helpful for identifying the genomic regions that contribute to traits, for estimating the extent of variation and the genetic action (i.e., additive, dominant, or epistatic) underlying this variation, and for pinpointing genetic correlations between traits. The aim of this paper is to review the recently published studies on QTL mapping with a particular emphasis on mapping populations used as well as traits related to kernel quality. We found that several populations have been used for QTL mapping including interspecific populations developed from crosses between synthetic tetraploids and elite varieties. Those populations allowed the broadening of the genetic base of cultivated peanut and helped with the mapping of QTL and identifying beneficial wild alleles for economically important traits. Furthermore, only a few studies reported QTL related to kernel quality. The main quality traits for which QTL have been mapped include oil and protein content as well as fatty acid compositions. QTL for other agronomic traits have also been reported. Among the 1261 QTL reported in this review, and extracted from the most relevant studies on QTL mapping in peanut, 413 (~33%) were related to kernel quality showing the importance of quality in peanut genetics and breeding. Exploiting the QTL information could accelerate breeding to develop highly nutritious superior cultivars in the face of climate change.
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Affiliation(s)
- Fentanesh C Kassie
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
- Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo P.O. Box 138, Ethiopia
| | - Joël R Nguepjop
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Hermine B Ngalle
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
| | - Dekoum V M Assaha
- Department of Agriculture, Higher Technical Teachers Training College, University of Buea, Kumba P.O. Box 249, Cameroon
| | - Mesfin K Gessese
- Department of Plant Science, College of Agriculture, Wolaita Sodo University, Sodo P.O. Box 138, Ethiopia
| | - Wosene G Abtew
- Department of Horticulture and Plant Science, College of Agriculture and Veterinary Medicine, Jimma University, Jimma P.O. Box 378, Ethiopia
| | - Hodo-Abalo Tossim
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Aissatou Sambou
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Maguette Seye
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Jean-François Rami
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Daniel Fonceka
- UMR AGAP, CIRAD, F-34398 Montpellier, France
- AGAP Institute, Institut Agro, CIRAD, INRAE, University of Montpellier, F-34060 Montpellier, France
- Centre d'Etudes Régional Pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS/ISRA), Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l'Ouest (IAVAO), CERAAS, Route de Khombole, Thiès BP 3320, Senegal
| | - Joseph M Bell
- Department of Plant Biology and Physiology, Faculty of Sciences, University of Yaounde I, Yaounde P.O. Box 337, Cameroon
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16
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Chen H, Yang X, Xu R, Chen X, Zhong H, Liu N, Huang L, Luo H, Huai D, Liu W, Chen Y, Chen J, Jiang H. Genetic mapping of AhVt1, a novel genetic locus that confers the variegated testa color in cultivated peanut ( Arachis hypogaea L.) and its utilization for marker-assisted selection. FRONTIERS IN PLANT SCIENCE 2023; 14:1145098. [PMID: 37021305 PMCID: PMC10067746 DOI: 10.3389/fpls.2023.1145098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Peanut (Arachis hypogaea L.) is an important cash crop worldwide. Compared with the ordinary peanut with pure pink testa, peanut with variegated testa color has attractive appearance and a higher market value. In addition, the variegated testa represents a distinct regulation pattern of anthocyanin accumulation in integument cells. METHODS In order to identify the genetic locus underlying variegated testa color in peanut, two populations were constructed from the crosses between Fuhua 8 (pure-pink testa) and Wucai (red on white variegated testa), Quanhonghua 1 (pure-red testa) and Wucai, respectively. Genetic analysis and bulked sergeant analysis sequencing were applied to detect and identify the genetic locus for variegated testa color. Marker-assisted selection was used to develop new variegated testa peanut lines. RESULTS As a result, all the seeds harvested from the F1 individuals of both populations showed the variegated testa type with white trace. Genetic analysis revealed that the pigmentation of colored region in red on white variegated testa was controlled by a previous reported gene AhRt1, while the formation of white region (un-pigmented region) in variegated testa was controlled by another single genetic locus. This locus, named as AhVt1 (Arachis hypogaea Variegated Testa 1), was preliminary mapped on chromosome 08 through bulked sergeant analysis sequencing. Using a secondary mapping population derived from the cross between Fuhua 8 and Wucai, AhVt1 was further mapped to a 1.89-Mb genomic interval by linkage analysis, and several potential genes associated with the uneven distribution of anthocyanin, such as MADS-box, MYB, and Chalcone synthase-like protein, were harbored in the region. Moreover, the molecular markers closely linked to the AhVt1 were developed, and the new variegated testa peanut lines were obtained with the help of marker-assisted selection. CONCLUSION Our findings will accelerate the breeding program for developing new peanut varieties with "colorful" testa colors and laid a foundation for map-based cloning of gene responsible for variegated testa.
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Affiliation(s)
- Hao Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Xinlei Yang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Rirong Xu
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
| | - Xiangyu Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
| | - Haifeng Zhong
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
| | - Nian Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Li Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Huaiyong Luo
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Dongxin Huai
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Wenjing Liu
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fujian Key Laboratory of Agro-products Quality and Safety, Fuzhou, China
| | - Yuhua Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
| | - Jianhong Chen
- R&D Center for Oil Crops, Quanzhou Institute of Agricultural Sciences, Jinjiang, China
| | - Huifang Jiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
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17
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Gangurde SS, Pasupuleti J, Parmar S, Variath MT, Bomireddy D, Manohar SS, Varshney RK, Singam P, Guo B, Pandey MK. Genetic mapping identifies genomic regions and candidate genes for seed weight and shelling percentage in groundnut. Front Genet 2023; 14:1128182. [PMID: 37007937 PMCID: PMC10061104 DOI: 10.3389/fgene.2023.1128182] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Seed size is not only a yield-related trait but also an important measure to determine the commercial value of groundnut in the international market. For instance, small size is preferred in oil production, whereas large-sized seeds are preferred in confectioneries. In order to identify the genomic regions associated with 100-seed weight (HSW) and shelling percentage (SHP), the recombinant inbred line (RIL) population (Chico × ICGV 02251) of 352 individuals was phenotyped for three seasons and genotyped with an Axiom_Arachis array containing 58K SNPs. A genetic map with 4199 SNP loci was constructed, spanning a map distance of 2708.36 cM. QTL analysis identified six QTLs for SHP, with three consistent QTLs on chromosomes A05, A08, and B10. Similarly, for HSW, seven QTLs located on chromosomes A01, A02, A04, A10, B05, B06, and B09 were identified. BIG SEED locus and spermidine synthase candidate genes associated with seed weight were identified in the QTL region on chromosome B09. Laccase, fibre protein, lipid transfer protein, senescence-associated protein, and disease-resistant NBS-LRR proteins were identified in the QTL regions associated with shelling percentage. The associated markers for major-effect QTLs for both traits successfully distinguished between the small- and large-seeded RILs. QTLs identified for HSW and SHP can be used for developing potential selectable markers to improve the cultivars with desired seed size and shelling percentage to meet the demands of confectionery industries.
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Affiliation(s)
- Sunil S. Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
- USDA-ARS, Crops Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Janila Pasupuleti
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sejal Parmar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Murali T. Variath
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Deekshitha Bomireddy
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surendra S. Manohar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Baozhu Guo
- USDA-ARS, Crops Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
- *Correspondence: Manish K. Pandey,
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18
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Cai L, Comont D, MacGregor D, Lowe C, Beffa R, Neve P, Saski C. The blackgrass genome reveals patterns of non-parallel evolution of polygenic herbicide resistance. THE NEW PHYTOLOGIST 2023; 237:1891-1907. [PMID: 36457293 PMCID: PMC10108218 DOI: 10.1111/nph.18655] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 11/23/2022] [Indexed: 05/31/2023]
Abstract
Globally, weedy plants are a major constraint to sustainable crop production. Much of the success of weeds rests with their ability to rapidly adapt in the face of human-mediated management of agroecosystems. Alopecurus myosuroides (blackgrass) is a widespread and impactful weed affecting agriculture in Europe. Here we report a chromosome-scale genome assembly of blackgrass and use this reference genome to explore the genomic/genetic basis of non-target site herbicide resistance (NTSR). Based on our analysis of F2 seed families derived from two distinct blackgrass populations with the same NTSR phenotype, we demonstrate that the trait is polygenic and evolves from standing genetic variation. We present evidence that selection for NTSR has signatures of both parallel and non-parallel evolution. There are parallel and non-parallel changes at the transcriptional level of several stress- and defence-responsive gene families. At the genomic level, however, the genetic loci underpinning NTSR are different (non-parallel) between seed families. We speculate that variation in the number, regulation and function of stress- and defence-related gene families enable weedy species to rapidly evolve NTSR via exaptation of genes within large multi-functional gene families. These results provide novel insights into the potential for, and nature of plant adaptation in rapidly changing environments.
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Affiliation(s)
- Lichun Cai
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - David Comont
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Dana MacGregor
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Claudia Lowe
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
| | - Roland Beffa
- Bayer Crop SciencesIndustriepark Höchst65926Frankfurt am MainGermany
- Königsteiner Weg 465835LiederbachGermany
| | - Paul Neve
- Protecting Crops and the EnvironmentRothamsted ResearchHarpenden, HertfordshireAL5 2JQUK
- Department of Plant and Environmental SciencesUniversity of CopenhagenHøjbakkegård Allé 13Tåstrup2630Denmark
| | - Christopher Saski
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
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19
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Genome-Wide Investigation of Apyrase (APY) Genes in Peanut ( Arachis hypogaea L.) and Functional Characterization of a Pod-Abundant Expression Promoter AhAPY2-1p. Int J Mol Sci 2023; 24:ijms24054622. [PMID: 36902052 PMCID: PMC10003104 DOI: 10.3390/ijms24054622] [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: 12/14/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 03/06/2023] Open
Abstract
Peanut (Arachis hypogaea L.) is an important food and feed crop worldwide and is affected by various biotic and abiotic stresses. The cellular ATP levels decrease significantly during stress as ATP molecules move to extracellular spaces, resulting in increased ROS production and cell apoptosis. Apyrases (APYs) are the nucleoside phosphatase (NPTs) superfamily members and play an important role in regulating cellular ATP levels under stress. We identified 17 APY homologs in A. hypogaea (AhAPYs), and their phylogenetic relationships, conserved motifs, putative miRNAs targeting different AhAPYs, cis-regulatory elements, etc., were studied in detail. The transcriptome expression data were used to observe the expression patterns in different tissues and under stress conditions. We found that the AhAPY2-1 gene showed abundant expression in the pericarp. As the pericarp is a key defense organ against environmental stress and promoters are the key elements regulating gene expression, we functionally characterized the AhAPY2-1 promoter for its possible use in future breeding programs. The functional characterization of AhAPY2-1P in transgenic Arabidopsis plants showed that it effectively regulated GUS gene expression in the pericarp. GUS expression was also detected in flowers of transgenic Arabidopsis plants. Overall, these results strongly suggest that APYs are an important future research subject for peanut and other crops, and AhPAY2-1P can be used to drive the resistance-related genes in a pericarp-specific manner to enhance the defensive abilities of the pericarp.
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20
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Pannak S, Wanchana S, Aesomnuk W, Pitaloka MK, Jamboonsri W, Siangliw M, Meyers BC, Toojinda T, Arikit S. Functional Bph14 from Rathu Heenati promotes resistance to BPH at the early seedling stage of rice (Oryza sativa L.) as revealed by QTL-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:25. [PMID: 36781491 DOI: 10.1007/s00122-023-04318-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
A QTL associated with BPH resistance at the early seedling stage was identified on chromosome 3. Functional Bph14 in Rathu Heenati was associated with BPH resistance at the early seedling stage. Brown planthopper (BPH; Nilaparvata lugens Stål) is considered the most important rice pest in many Asian countries. Several BPH resistance genes have previously been identified. However, there are few reports of genes specific for BPH resistance at the early seedling stage, a crucial stage for direct-seeding cultivation. In this study, we performed a QTL-seq analysis using two bulks (20 F2 lines in each bulk) of the F2 population (n = 300) derived from a cross of Rathu Heenati (RH) × HCS-1 to identify QTL/genes associated with BPH resistance at the early seedling stage. An important QTL was identified on chromosome 3 and Bph14 was identified as a potential candidate gene based on the differences in gene expression and sequence variation when compared with the two parents. All plants in the resistant bulks possessed the functional Bph14 from RH and all plants in the susceptible bulk and HCS-1 contained a large deletion (2703 bp) in Bph14. The functional Bph14 gene of RH appears to be important for BPH resistance at the early seedling stage of rice and could be used in conjunction with other BPH resistance genes in rice breeding programs that confer resistance to BPH at the early and later growth stages.
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Affiliation(s)
- Sarinthip Pannak
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Center of Excellence On Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok, 10900, Thailand
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Wanchana Aesomnuk
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Mutiara K Pitaloka
- Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Watchareewan Jamboonsri
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, 12120, PathumThani, Thailand
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
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21
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Yang Q, Sharif Y, Zhuang Y, Chen H, Zhang C, Fu H, Wang S, Cai T, Chen K, Raza A, Wang L, Zhuang W. Genome-wide identification of germin-like proteins in peanut ( Arachis hypogea L.) and expression analysis under different abiotic stresses. FRONTIERS IN PLANT SCIENCE 2023; 13:1044144. [PMID: 36756235 PMCID: PMC9901545 DOI: 10.3389/fpls.2022.1044144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
Peanut is an important food and feed crop, providing oil and protein nutrients. Germins and germin-like proteins (GLPs) are ubiquitously present in plants playing numerous roles in defense, growth and development, and different signaling pathways. However, the GLP members have not been comprehensively studied in peanut at the genome-wide scale. We carried out a genome-wide identification of the GLP genes in peanut genome. GLP members were identified comprehensively, and gene structure, genomic positions, motifs/domains distribution patterns, and phylogenetic history were studied in detail. Promoter Cis-elements, gene duplication, collinearity, miRNAs, protein-protein interactions, and expression were determined. A total of 84 GLPs (AhGLPs ) were found in the genome of cultivated peanut. These GLP genes were clustered into six groups. Segmental duplication events played a key role in the evolution of AhGLPs, and purifying selection pressure was underlying the duplication process. Most AhGLPs possessed a well-maintained gene structure and motif organization within the same group. The promoter regions of AhGLPs contained several key cis-elements responsive to 'phytohormones', 'growth and development', defense, and 'light induction'. Seven microRNAs (miRNAs) from six families were found targeting 25 AhGLPs. Gene Ontology (GO) enrichment analysis showed that AhGLPs are highly enriched in nutrient reservoir activity, aleurone grain, external encapsulating structure, multicellular organismal reproductive process, and response to acid chemicals, indicating their important biological roles. AhGLP14, AhGLP38, AhGLP54, and AhGLP76 were expressed in most tissues, while AhGLP26, AhGLP29, and AhGLP62 showed abundant expression in the pericarp. AhGLP7, AhGLP20, and AhGLP21, etc., showed specifically high expression in embryo, while AhGLP12, AhGLP18, AhGLP40, AhGLP78, and AhGLP82 were highly expressed under different hormones, water, and temperature stress. The qRT-PCR results were in accordance with the transcriptome expression data. In short, these findings provided a foundation for future functional investigations on the AhGLPs for peanut breeding programs.
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Affiliation(s)
- Qiang Yang
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Yasir Sharif
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Yuhui Zhuang
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Hua Chen
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Chong Zhang
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Huiwen Fu
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Shanshan Wang
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Tiecheng Cai
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Kun Chen
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Ali Raza
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
| | - Lihui Wang
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Weijian Zhuang
- Center of Legume Plant Genetics and System Biology, College of Agronomy, College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
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22
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Guo J, Qi F, Qin L, Zhang M, Sun Z, Li H, Cui M, Zhang M, Li C, Li X, Zhao Q, Luo D, Tian M, Liu H, Xu J, Miao L, Huang B, Dong W, Han S, Zhang X. Mapping of a QTL associated with sucrose content in peanut kernels using BSA-seq. Front Genet 2023; 13:1089389. [PMID: 36685909 PMCID: PMC9845247 DOI: 10.3389/fgene.2022.1089389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
As an important factor affecting the edible quality of peanut kernels, sucrose content is a complex quantitative trait regulated by multiple factors. In this study, an F2 segregating population and a recombinant inbred line (RIL) population, derived from a cross between the high sucrose content variety Jihuatian 1 and the low sucrose content line PI478819, were used as materials to map a quantitative trait locus (QTL) associated with sucrose content in peanut kernels. Four QTLs were initially located on chromosomes A03 and A06 based on BSA-seq technology, and multiple kompetitive allele-specific PCR markers were developed based on single-nucleotide polymorphisms (SNPs) in the intervals. The markers were genotyped in the RIL population and finely mapped to a stable QTL, qSUCA06, located on chromosome A06 within a 0.29-Mb physical genomic interval (112367085-112662675 bp), which accounted for 31.95%-41.05% of the phenotypic variance explained. SNP and insertion/deletion annotations were performed on genes in the candidate interval, and having screened out those genes with mutations in exons, candidate genes were verified by qRT-PCR. The results revealed that Arahy.Y2LWD9 may be the main gene regulating sucrose content. The QTL identified in this study will not only contribute to marker-assisted breeding for improvement of peanut sucrose content but also paves the way for identifying gene function.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Suoyi Han
- *Correspondence: Xinyou Zhang, ; Suoyi Han,
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23
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Zhang C, Xie W, Fu H, Chen Y, Chen H, Cai T, Yang Q, Zhuang Y, Zhong X, Chen K, Gao M, Liu F, Wan Y, Pandey MK, Varshney RK, Zhuang W. Whole genome resequencing identifies candidate genes and allelic diagnostic markers for resistance to Ralstonia solanacearum infection in cultivated peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1048168. [PMID: 36684803 PMCID: PMC9845939 DOI: 10.3389/fpls.2022.1048168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Bacterial wilt disease (BWD), caused by Ralstonia solanacearum is a major challenge for peanut production in China and significantly affects global peanut field productivity. It is imperative to identify genetic loci and putative genes controlling resistance to R. solanacearum (RRS). Therefore, a sequencing-based trait mapping approach termed "QTL-seq" was applied to a recombination inbred line population of 581 individuals from the cross of Yueyou 92 (resistant) and Xinhuixiaoli (susceptible). A total of 381,642 homozygous single nucleotide polymorphisms (SNPs) and 98,918 InDels were identified through whole genome resequencing of resistant and susceptible parents for RRS. Using QTL-seq analysis, a candidate genomic region comprising of 7.2 Mb (1.8-9.0 Mb) was identified on chromosome 12 which was found to be significantly associated with RRS based on combined Euclidean Distance (ED) and SNP-index methods. This candidate genomic region had 180 nonsynonymous SNPs and 14 InDels that affected 75 and 11 putative candidate genes, respectively. Finally, eight nucleotide binding site leucine rich repeat (NBS-LRR) putative resistant genes were identified as the important candidate genes with high confidence. Two diagnostic SNP markers were validated and revealed high phenotypic variation in the different resistant and susceptible RIL lines. These findings advocate the expediency of the QTL-seq approach for precise and rapid identification of candidate genomic regions, and the development of diagnostic markers that are applicable in breeding disease-resistant peanut varieties.
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Affiliation(s)
- Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Wenping Xie
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiwen Fu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuting Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhui Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Zhong
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kun Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meijia Gao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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24
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Dhaliwal SK, Gill RK, Sharma A, Kaur A, Bhatia D, Kaur S. A large-effect QTL introgressed from ricebean imparts resistance to Mungbean yellow mosaic India virus in blackgram (Vigna mungo (L.) Hepper). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4495-4506. [PMID: 36271056 DOI: 10.1007/s00122-022-04234-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Here, we report identification of a large effect QTL conferring Mungbean yellow mosaic India virus resistance introgressed from ricebean in blackgram variety Mash114. The tightly linked KASP markers would assist in marker-assisted-transfer of this region into Vigna species infected by MYMIV. Until recently, precise location of genes and marker-assisted selection was long thought in legumes such as blackgram due to lack of dense molecular maps. However, advances in next-generation sequencing based on high-throughput genotyping technologies such as QTL-seq have revolutionized trait mapping in marker-orphan crops. Using QTL-seq approach, we have identified a large-effect QTL for resistance to Mungbean yellow mosaic India virus (MYMIV) in blackgram variety Mash114. MYMIV is devastating disease responsible for huge yield losses in blackgram, greengram and other legumes. Mash114 showed consistent and high level of resistance to MYMIV since last nine years. Whole genome re-sequencing of MYMIV-resistant and susceptible bulks derived from RILs of cross KUG253 X Mash114 identified a large-effect QTL (qMYMIV6.1.1) spanning 3.4 Mb on chromosome 6 explaining 70% of total phenotypic variation. This region was further identified as an inter-specific introgression from ricebean. Linkage mapping using KASP markers developed from potent candidate genes involved in virus resistance identified the 500 kb genomic region equaling 1.9 cM on genetic map linked with MYMIV. The three KASP markers closely associated with MYMIV originated from serine threonine kinase, UBE2D2 and BAK1/BRI1-ASSOCIATED RECEPTOR KINASE genes. These KASPs can be used for marker-assisted transfer of introgressed segment into suitable backgrounds of Vigna species.
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Affiliation(s)
- Sandeep Kaur Dhaliwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Ranjit Kaur Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Abhishek Sharma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.
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25
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Zhang H, Mascher M, Abbo S, Jayakodi M. Advancing Grain Legumes Domestication and Evolution Studies with Genomics. PLANT & CELL PHYSIOLOGY 2022; 63:1540-1553. [PMID: 35534441 PMCID: PMC9680859 DOI: 10.1093/pcp/pcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.
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Affiliation(s)
- Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig 04103, Germany
| | - Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
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26
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Raza A, Sharif Y, Chen K, Wang L, Fu H, Zhuang Y, Chitikineni A, Chen H, Zhang C, Varshney RK, Zhuang W. Genome-Wide Characterization of Ascorbate Peroxidase Gene Family in Peanut ( Arachis hypogea L.) Revealed Their Crucial Role in Growth and Multiple Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:962182. [PMID: 36186077 PMCID: PMC9524023 DOI: 10.3389/fpls.2022.962182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 06/16/2023]
Abstract
Ascorbate peroxidase (APX), an important antioxidant enzyme, plays a significant role in ROS scavenging by catalyzing the decrease of hydrogen peroxide under various environmental stresses. Nevertheless, information about the APX gene family and their evolutionary and functional attributes in peanut (Arachis hypogea L.) was not reported. Therefore, a comprehensive genome-wide study was performed to discover the APX genes in cultivated peanut genome. This study identified 166 AhAPX genes in the peanut genome, classified into 11 main groups. The gene duplication analysis showed that AhAPX genes had experienced segmental duplications and purifying selection pressure. Gene structure and motif investigation indicated that most of the AhAPX genes exhibited a comparatively well-preserved exon-intron pattern and motif configuration contained by the identical group. We discovered five phytohormones-, six abiotic stress-, and five growth and development-related cis-elements in the promoter regions of AhAPX. Fourteen putative ah-miRNAs from 12 families were identified, targeting 33 AhAPX genes. Furthermore, we identified 3,257 transcription factors from 38 families (including AP2, ARF, B3, bHLH, bZIP, ERF, MYB, NAC, WRKY, etc.) in 162 AhAPX genes. Gene ontology and KEGG enrichment analysis confirm the role of AhAPX genes in oxidoreductase activity, catalytic activity, cell junction, cellular response to stimulus and detoxification, biosynthesis of metabolites, and phenylpropanoid metabolism. Based on transcriptome datasets, some genes such as AhAPX4/7/17/77/82/86/130/133 and AhAPX160 showed significantly higher expression in diverse tissues/organs, i.e., flower, leaf, stem, roots, peg, testa, and cotyledon. Likewise, only a few genes, including AhAPX4/17/19/55/59/82/101/102/137 and AhAPX140, were significantly upregulated under abiotic (drought and cold), and phytohormones (ethylene, abscisic acid, paclobutrazol, brassinolide, and salicylic acid) treatments. qRT-PCR-based expression profiling presented the parallel expression trends as generated from transcriptome datasets. Our discoveries gave new visions into the evolution of APX genes and provided a base for further functional examinations of the AhAPX genes in peanut breeding programs.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Kun Chen
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Lihui Wang
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Huiwen Fu
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Annapurna Chitikineni
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Plant Genetics and Systems Biology, College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
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27
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Majeed A, Johar P, Raina A, Salgotra RK, Feng X, Bhat JA. Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding. Front Genet 2022; 13:944501. [PMID: 36003337 PMCID: PMC9393495 DOI: 10.3389/fgene.2022.944501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/28/2022] [Indexed: 12/26/2022] Open
Abstract
Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to which their efficiency in crop breeding is reduced. In this regard, the bulk segregant analysis sequencing (BSA-seq) and its related approaches, viz., quantitative trait locus (QTL)-seq, bulk segregant RNA-Seq (BSR)-seq, and MutMap, have emerged as efficient methods to identify the genomic loci/QTLs controlling specific traits at high resolution, accuracy, reduced time span, and in a high-throughput manner. These approaches combine BSA with next-generation sequencing (NGS) and enable the rapid identification of genetic loci for qualitative and quantitative assessments. Many previous studies have shown the successful identification of the genetic loci for different plant traits using BSA-seq and its related approaches, as discussed in the text with details. However, the efficiency and accuracy of the BSA-seq depend upon factors like sequencing depth and coverage, which enhance the sequencing cost. Recently, the rapid reduction in the cost of NGS together with the expected cost reduction of third-generation sequencing in the future has further increased the accuracy and commercial applicability of these approaches in crop improvement programs. This review article provides an overview of BSA-seq and its related approaches in crop breeding together with their merits and challenges in trait mapping.
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Affiliation(s)
- Aasim Majeed
- School of Agricultural Biotechnology, Punjab Agriculture University (PAU), Ludhiana, India
| | - Prerna Johar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Aamir Raina
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - R. K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | | | - Javaid Akhter Bhat
- Zhejiang Lab, Hangzhou, China
- International Genome Center, Jiangsu University, Zhenjiang, China
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28
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Song H, Guo Z, Zhang X, Sui J. De novo genes in Arachis hypogaea cv. Tifrunner: systematic identification, molecular evolution, and potential contributions to cultivated peanut. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1081-1095. [PMID: 35748398 DOI: 10.1111/tpj.15875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
De novo genes are derived from non-coding sequences, and they can play essential roles in organisms. Cultivated peanut (Arachis hypogaea) is a major oil and protein crop derived from a cross between Arachis duranensis and Arachis ipaensis. However, few de novo genes have been documented in Arachis. Here, we identified 381 de novo genes in A. hypogaea cv. Tifrunner based on comparison with five closely related Arachis species. There are distinct differences in gene expression patterns and gene structures between conserved and de novo genes. The identified de novo genes originated from ancestral sequence regions associated with metabolic and biosynthetic processes, and they were subsequently integrated into existing regulatory networks. De novo paralogs and homoeologs were identified in A. hypogaea cv. Tifrunner. De novo paralogs and homoeologs with conserved expression have mismatching cis-acting elements under normal growth conditions. De novo genes potentially have pluripotent functions in responses to biotic stresses as well as in growth and development based on quantitative trait locus data. This work provides a foundation for future research examining gene birth processes and gene function in Arachis and related taxa.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, 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, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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29
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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30
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Han S, Zhou X, Shi L, Zhang H, Geng Y, Fang Y, Xia H, Liu H, Li P, Zhao S, Miao L, Hou L, Zhang Z, Xu J, Ma C, Wang Z, Li H, Zheng Z, Huang B, Dong W, Zhang J, Tang F, Li S, Gao M, Zhang X, Zhao C, Wang X. AhNPR3 regulates the expression of WRKY and PR genes, and mediates the immune response of the peanut (Arachis hypogaea L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:735-747. [PMID: 35124871 DOI: 10.1111/tpj.15700] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Systemic acquired resistance is an essential immune response that triggers a broad-spectrum disease resistance throughout the plant. In the present study, we identified a peanut lesion mimic mutant m14 derived from an ethyl methane sulfonate-mutagenized mutant pool of peanut cultivar "Yuanza9102." Brown lesions were observed in the leaves of an m14 mutant from seedling stage to maturity. Using MutMap together with bulked segregation RNA analysis approaches, a G-to-A point mutation was identified in the exon region of candidate gene Arahy.R60CUW, which is the homolog of AtNPR3 (Nonexpresser of PR genes) in Arabidopsis. This point mutation caused a transition from Gly to Arg within the C-terminal transactivation domain of AhNPR3A. The mutation of AhNPR3A showed no effect in the induction of PR genes when treated with salicylic acid. Instead, the mutation resulted in upregulation of WRKY genes and several PR genes, including pathogenesis-related thaumatin- and chitinase-encoding genes, which is consistent with the resistant phenotype of m14 to leaf spot disease. Further study on the AhNPR3A gene will provide valuable insights into understanding the molecular mechanism of systemic acquired resistance in peanut. Moreover, our results indicated that a combination of MutMap and bulked segregation RNA analysis is an effective method for identifying genes from peanut mutants.
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Affiliation(s)
- Suoyi Han
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Ximeng Zhou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Lei Shi
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Huayang Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Yun Geng
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Yuanjin Fang
- Kaifeng Academy of Agriculture and Forestry, Kaifeng, 475000, China
| | - Han Xia
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Hua Liu
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Lijuan Miao
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Lei Hou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhongxin Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jing Xu
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Hongyan Li
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Zheng Zheng
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Bingyan Huang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jun Zhang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Fengshou Tang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Shaojian Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Meng Gao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Xinyou Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
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31
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Insights into the Genomic Architecture of Seed and Pod Quality Traits in the U.S. Peanut Mini-Core Diversity Panel. PLANTS 2022; 11:plants11070837. [PMID: 35406817 PMCID: PMC9003526 DOI: 10.3390/plants11070837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022]
Abstract
Traits such as seed weight, shelling percent, percent sound mature kernels, and seed dormancy determines the quality of peanut seed. Few QTL (quantitative trait loci) studies using biparental mapping populations have identified QTL for seed dormancy and seed grade traits. Here, we report a genome-wide association study (GWAS) to detect marker–trait associations for seed germination, dormancy, and seed grading traits in peanut. A total of 120 accessions from the U.S. peanut mini-core collection were evaluated for seed quality traits and genotyped using Axiom SNP (single nucleotide polymorphism) array for peanut. We observed significant variation in seed quality traits in different accessions and different botanical varieties. Through GWAS, we were able to identify multiple regions associated with sound mature kernels, seed weight, shelling percent, seed germination, and dormancy. Some of the genomic regions that were SNP associated with these traits aligned with previously known QTLs. For instance, QTL for seed dormancy has been reported on chromosome A05, and we also found SNP on the same chromosome associated with seed dormancy, explaining around 20% of phenotypic variation. In addition, we found novel genomic regions associated with seed grading, seed germination, and dormancy traits. SNP markers associated with seed quality and dormancy identified here can accelerate the selection process. Further, exploring the function of candidate genes identified in the vicinity of the associated marker will assist in understanding the complex genetic network that governs seed quality.
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32
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QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea. Heredity (Edinb) 2022; 128:411-419. [PMID: 35022582 PMCID: PMC9177671 DOI: 10.1038/s41437-021-00486-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 12/20/2022] Open
Abstract
To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement. QTL-seq approach was utilized for mapping of genomic regions/genes associated with days to flowering and leaf shape in pigeonpea. Analysis of genomic regions and associated SNPs with days to flowering and leaf shape revealed 1 and 4 non-synonymous SNPs, respectively. The study demonstrated sequencing-based trait mapping approach can accelerate trait mapping of the targeted traits.
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Ma Y, Liu D, Wariss HM, Zhang R, Tao L, Milne RI, Sun W. Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple. Mol Ecol 2021; 31:767-779. [PMID: 34826164 DOI: 10.1111/mec.16289] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 12/01/2022]
Abstract
Recent advancements in whole genome sequencing techniques capable of covering nearly all the nucleotide variations of a genome would make it possible to set up a conservation framework for threatened plants at the genomic level. Here we applied a whole genome resequencing approach to obtain genome-wide data from 105 individuals sampled from the 10 currently known extant populations of Acer yangbiense, an endangered species with fragmented habitats and restricted distribution in Yunnan, China. To inform meaningful conservation action, we investigated what factors might have contributed to the formation of its extremely small population sizes and what threats it currently suffers at a genomic level. Our results revealed that A. yangbiense has low genetic diversity and comprises different numbers of genetic groups based on neutral (seven) and selected loci (13), with frequent gene flow between populations. Repeated bottleneck events, particularly the most recent one occurring within ~10,000 years before present, which decreased its effective population size (Ne ) < 200, and severe habitat fragmentation resulting from anthropogenic activities as well as a biased gender ratio of mature individuals in its natural habitat, might have together contributed to the currently fragmented and endangered status of A. yangbiense. The species has suffered from inbreeding and deleterious mutation load, both of which varied among populations but had similar patterns; that is, populations with higher FROH (frequency of runs of homozygosity) always carried a larger number of deleterious mutations in the homozygous state than in populations with lower FROH. In addition, based on our genetic differentiation results, and the distribution patterns of homozygous deleterious mutations in individuals, we recommend certain conservation actions regarding the genetic rescue of A. yangbiense. Overall, our study provides meaningful insights into the conservation genetics and a framework for the further conservation for the endangered A. yangbiense.
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Affiliation(s)
- Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hafiz Muhammad Wariss
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
| | - Rengang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, China
| | - Lidan Tao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China.,Kunming Botanical Garden, Chinese Academy of Sciences, Kunming Institute of Botany, Kunming, China
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Thianthavon T, Aesomnuk W, Pitaloka MK, Sattayachiti W, Sonsom Y, Nubankoh P, Malichan S, Riangwong K, Ruanjaichon V, Toojinda T, Wanchana S, Arikit S. Identification and Validation of a QTL for Bacterial Leaf Streak Resistance in Rice ( Oryza sativa L.) against Thai Xoc Strains. Genes (Basel) 2021; 12:1587. [PMID: 34680982 PMCID: PMC8535723 DOI: 10.3390/genes12101587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 11/17/2022] Open
Abstract
Rice is one of the most important food crops in the world and is of vital importance to many countries. Various diseases caused by fungi, bacteria and viruses constantly threaten rice plants and cause yield losses. Bacterial leaf streak disease (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most devastating rice diseases. However, most modern rice varieties are susceptible to BLS. In this study, we applied the QTL-seq approach using an F2 population derived from the cross between IR62266 and Homcholasit (HSC) to rapidly identify the quantitative trait loci (QTL) that confers resistance to BLS caused by a Thai Xoc isolate, SP7-5. The results showed that a single genomic region at the beginning of chromosome 5 was highly associated with resistance to BLS. The gene xa5 was considered a potential candidate gene in this region since most associated single nucleotide polymorphisms (SNPs) were within this gene. A Kompetitive Allele-Specific PCR (KASP) marker was developed based on two consecutive functional SNPs in xa5 and validated in six F2 populations inoculated with another Thai Xoc isolate, 2NY2-2. The phenotypic variance explained by this marker (PVE) ranged from 59.04% to 70.84% in the six populations. These findings indicate that xa5 is a viable candidate gene for BLS resistance and may help in breeding programs for BLS resistance.
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Affiliation(s)
- Tripop Thianthavon
- Plant Breeding Program, Faculty of Agriculture at Kamphaeng Saen, Kesetsart University, Nakhon Pathom 73140, Thailand;
| | - Wanchana Aesomnuk
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Mutiara K. Pitaloka
- Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
| | - Wannapa Sattayachiti
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Yupin Sonsom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Phakchana Nubankoh
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Srihunsa Malichan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand;
| | - Kanamon Riangwong
- Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Sanamchandra Palace Campus, Nakhon Pathom 73000, Thailand;
| | - Vinitchan Ruanjaichon
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand; (W.A.); (W.S.); (Y.S.); (P.N.); (V.R.); (T.T.)
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
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Kumar R, Sharma V, Suresh S, Ramrao DP, Veershetty A, Kumar S, Priscilla K, Hangargi B, Narasanna R, Pandey MK, Naik GR, Thomas S, Kumar A. Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples. Front Genet 2021; 12:637141. [PMID: 33889179 PMCID: PMC8055929 DOI: 10.3389/fgene.2021.637141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/02/2021] [Indexed: 01/07/2023] Open
Abstract
In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.
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Affiliation(s)
- Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Srinivas Suresh
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Akash Veershetty
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Sharan Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Kagolla Priscilla
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | | | - Rahul Narasanna
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Manish Kumar Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Sherinmol Thomas
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University, Amarkantak, India
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Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Zhang C, Badri Anarjan M, Win KT, Begum S, Lee S. QTL-seq analysis of powdery mildew resistance in a Korean cucumber inbred line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:435-451. [PMID: 33070226 DOI: 10.1007/s00122-020-03705-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
QTL mapping and RT-PCR analyses identified the CsGy5G015660 as a strong powdery mildew resistance candidate gene and natural variation of CsGy5G015660 allele was observed using 115 core germplasm. Powdery mildew (PM) is among the most serious fungal diseases encountered in the cultivation of cucurbits. The development of PM-resistant inbred lines is thus of considerable significance for cucumber breeding programs. In this study, we applied bulked segregant analysis combined with QTL-seq to identify PM resistance loci using F2 population derived from a cross between two Korean cucumber inbred lines, PM-R (resistant) and PM-S (susceptible). Genome-wide SNP profiling using bulks of the two extreme phenotypes identified two QTLs on chromosomes 5 and 6, designated pm5.2 and pm6.1, respectively. The two PM resistance loci were validated using molecular marker-based classical QTL analysis: pm5.2 (30% R2 at LOD 11) and pm6.1 (11% R2 at LOD 3.2). Furthermore, reverse transcriptase-PCR analyses, using genes found to be polymorphic between PM-R and PM-S, were conducted to identify the candidate gene(s) responsible for PM resistance. We found that transcripts of the gene CsGy5G015660, encoding a putative leucine-rich repeat receptor-like serine/threonine-protein kinase (RPK2), showed specific accumulation in PM-R prior to the appearance of disease symptoms, and was accordingly considered a strong candidate gene for PM resistance. In addition, cleaved amplified polymorphic sequence markers from CsGy5G015660 were developed and used to screen 35 inbred lines. Natural variation in the CsGy5G015660 allele was also observed based on analysis of a core collection of 115 cucumber accessions. Our results provide new genetic insights for gaining a better understanding of the genetic basis of PM resistance in cucumber, and pave the way for further utilization in cucumber PM resistance breeding programs.
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Affiliation(s)
- Chunying Zhang
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea
- Department of Integrated Bioindustry, Graduate School of Hanseo University, 46 hanseo 1-ro, Haemi-myun, Seosan-si, Chungcheongnam-do, 31962, Republic of Korea
| | - Mahdi Badri Anarjan
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea
| | - Khin Thanda Win
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea
| | - Shahida Begum
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea
| | - Sanghyeob Lee
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea.
- Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea.
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Bohra A, Chand Jha U, Godwin ID, Kumar Varshney R. Genomic interventions for sustainable agriculture. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2388-2405. [PMID: 32875704 PMCID: PMC7680532 DOI: 10.1111/pbi.13472] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/21/2020] [Accepted: 08/16/2020] [Indexed: 05/05/2023]
Abstract
Agricultural production faces a Herculean challenge to feed the increasing global population. Food production systems need to deliver more with finite land and water resources while exerting the least negative influence on the ecosystem. The unpredictability of climate change and consequent changes in pests/pathogens dynamics aggravate the enormity of the challenge. Crop improvement has made significant contributions towards food security, and breeding climate-smart cultivars are considered the most sustainable way to accelerate food production. However, a fundamental change is needed in the conventional breeding framework in order to respond adequately to the growing food demands. Progress in genomics has provided new concepts and tools that hold promise to make plant breeding procedures more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing delineate breeding targets that could contribute to securing future food supply. In this review, we highlight key breakthroughs in plant genome sequencing and explain how the presence of these genome resources in combination with gene editing techniques has revolutionized the procedures of trait discovery and manipulation. Adoption of new approaches such as speed breeding, genomic selection and haplotype-based breeding could overcome several limitations of conventional breeding. We advocate that strengthening varietal release and seed distribution systems will play a more determining role in delivering genetic gains at farmer's field. A holistic approach outlined here would be crucial to deliver steady stream of climate-smart crop cultivars for sustainable agriculture.
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Affiliation(s)
- Abhishek Bohra
- ICAR‐Indian Institute of Pulses Research (IIPR)KanpurIndia
| | - Uday Chand Jha
- ICAR‐Indian Institute of Pulses Research (IIPR)KanpurIndia
| | - Ian D. Godwin
- Centre for Crop ScienceQueensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Rajeev Kumar Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthAustralia
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Gangurde SS, Wang H, Yaduru S, Pandey MK, Fountain JC, Chu Y, Isleib T, Holbrook CC, Xavier A, Culbreath AK, Ozias‐Akins P, Varshney RK, Guo B. Nested-association mapping (NAM)-based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1457-1471. [PMID: 31808273 PMCID: PMC7206994 DOI: 10.1111/pbi.13311] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 05/05/2023]
Abstract
Multiparental genetic mapping populations such as nested-association mapping (NAM) have great potential for investigating quantitative traits and associated genomic regions leading to rapid discovery of candidate genes and markers. To demonstrate the utility and power of this approach, two NAM populations, NAM_Tifrunner and NAM_Florida-07, were used for dissecting genetic control of 100-pod weight (PW) and 100-seed weight (SW) in peanut. Two high-density SNP-based genetic maps were constructed with 3341 loci and 2668 loci for NAM_Tifrunner and NAM_Florida-07, respectively. The quantitative trait locus (QTL) analysis identified 12 and 8 major effect QTLs for PW and SW, respectively, in NAM_Tifrunner, and 13 and 11 major effect QTLs for PW and SW, respectively, in NAM_Florida-07. Most of the QTLs associated with PW and SW were mapped on the chromosomes A05, A06, B05 and B06. A genomewide association study (GWAS) analysis identified 19 and 28 highly significant SNP-trait associations (STAs) in NAM_Tifrunner and 11 and 17 STAs in NAM_Florida-07 for PW and SW, respectively. These significant STAs were co-localized, suggesting that PW and SW are co-regulated by several candidate genes identified on chromosomes A05, A06, B05, and B06. This study demonstrates the utility of NAM population for genetic dissection of complex traits and performing high-resolution trait mapping in peanut.
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Affiliation(s)
- Sunil S. Gangurde
- International 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
| | - Shasidhar Yaduru
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Manish K. Pandey
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jake C. Fountain
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Ye Chu
- Horticulture DepartmentUniversity of GeorgiaTiftonGAUSA
| | - Thomas Isleib
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNCUSA
| | | | | | | | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Baozhu Guo
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
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40
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Pandey MK, Pandey AK, Kumar R, Nwosu CV, Guo B, Wright GC, Bhat RS, Chen X, Bera SK, Yuan M, Jiang H, Faye I, Radhakrishnan T, Wang X, Liang X, Liao B, Zhang X, Varshney RK, Zhuang W. Translational genomics for achieving higher genetic gains in groundnut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1679-1702. [PMID: 32328677 PMCID: PMC7214508 DOI: 10.1007/s00122-020-03592-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 04/01/2020] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Groundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- University of Southern Queensland (USQ), Toowoomba, Australia.
| | - Arun K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rakesh Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Central University of Karnataka, Gulbarga, India
| | | | - Baozhu Guo
- Crop Protection and Management Research Unit, United State Department of Agriculture - Agricultural Research Service (USDA-ARS), Tifton, USA
| | - Graeme C Wright
- University of Southern Queensland (USQ), Toowoomba, Australia
- Peanut Company of Australia (PCA), Kingaroy, Australia
| | - Ramesh S Bhat
- University of Agricultural Sciences (UAS), Dharwad, India
| | - Xiaoping Chen
- Crops Research Institute (CRI), Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China
| | - Sandip K Bera
- ICAR-Directorate of Groundnut Research (DGR), Junagadh, India
| | - Mei Yuan
- Shandong Peanut Research Institute (SPRI), Qingdao, China
| | - Huifang Jiang
- Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Issa Faye
- Institut Sénégalais de Recherches Agricoles (ISRA)-Centre National de Recherches Agronomiques (CNRA), Bambey, Senegal
| | | | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Xuanquiang Liang
- Crops Research Institute (CRI), Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, China
| | - Boshou Liao
- Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences (HAAS), Zhenzhou, China
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Weijian Zhuang
- Institute of Oil Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Jaganathan D, Bohra A, Thudi M, Varshney RK. Fine mapping and gene cloning in the post-NGS era: advances and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1791-1810. [PMID: 32040676 PMCID: PMC7214393 DOI: 10.1007/s00122-020-03560-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/29/2020] [Indexed: 05/18/2023]
Abstract
Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
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Affiliation(s)
- Deepa Jaganathan
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Abhishek Bohra
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
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