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Wu X, Hu Z, Zhang Y, Li M, Liao N, Dong J, Wang B, Wu J, Wu X, Wang Y, Wang J, Lu Z, Yang Y, Sun Y, Dong W, Zhang M, Li G. Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement. Nat Genet 2024; 56:992-1005. [PMID: 38649710 DOI: 10.1038/s41588-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas.
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Affiliation(s)
- Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongyuan Hu
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Yan Zhang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Mao Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Nanqiao Liao
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Junyang Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Baogen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Xiaohua Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Ying Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongfu Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Yi Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Yuyan Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Wenqi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Mingfang Zhang
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China.
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, P. R. China.
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, P. R. China.
| | - Guojing Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
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Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
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Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
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Li M, Wu X, Wang B, Wu X, Wang Y, Wang J, Dong J, Wu J, Lu Z, Sun Y, Dong W, Yang J, Li G. Genome-wide association analysis reveals the optimal genomic regions for pod size in bean. FRONTIERS IN PLANT SCIENCE 2023; 14:1138988. [PMID: 37251758 PMCID: PMC10213521 DOI: 10.3389/fpls.2023.1138988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/28/2023] [Indexed: 05/31/2023]
Abstract
The snap bean is the most commonly grown vegetable legume worldwide, and its pod size is both an important yield and appearance quality trait. However, the improvement of pod size in snap beans grown in China has been largely hindered by a lack of information on the specific genes that determine pod size. In this study, we identified 88 snap bean accessions and evaluated their pod size traits. Through a genome-wide association study (GWAS), 57 single nucleotide polymorphisms (SNPs) significantly associated with pod size were detected. Candidate gene analysis showed that cytochrome P450 family genes, WRKY, and MYB transcription factors were the predominant candidate genes for pod development, and eight of these 26 candidate genes showed relatively higher expression patterns in flowers and young pods. A significant pod length (PL) SNP and a single pod weight (SPW) SNP were successfully converted into kompetitive allele-specific polymerase chain reaction (KASP) markers and validated in the panel. These results enhance our understanding of the genetic basis of pod size, and also provide genetic resources for the molecular breeding of pod size in snap beans.
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Affiliation(s)
- Mao Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou, China
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Junyang Dong
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou, China
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Wu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou, China
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuyan Sun
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenqi Dong
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jing Yang
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A & F University, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Fang P, Sun T, Pandey AK, Jiang L, Wu X, Hu Y, Cheng S, Li M, Xu P. Understanding water conservation vs. profligation traits in vegetable legumes through a physio-transcriptomic-functional approach. HORTICULTURE RESEARCH 2023; 10:uhac287. [PMID: 36938572 PMCID: PMC10015340 DOI: 10.1093/hr/uhac287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Vegetable soybean and cowpea are related warm-season legumes showing contrasting leaf water use behaviors under similar root drought stresses, whose mechanisms are not well understood. Here we conducted an integrative phenomic-transcriptomic study on the two crops grown in a feedback irrigation system that enabled precise control of soil water contents. Continuous transpiration rate monitoring demonstrated that cowpea used water more conservatively under earlier soil drought stages, but tended to maintain higher transpiration under prolonged drought. Interestingly, we observed a soybean-specific transpiration rate increase accompanied by phase shift under moderate soil drought. Time-series transcriptomic analysis suggested a dehydration avoidance mechanism of cowpea at early soil drought stage, in which the VuHAI3 and VuTIP2;3 genes were suggested to be involved. Multifactorial gene clustering analysis revealed different responsiveness of genes to drought, time of day and their interactions between the two crops, which involved species-dependent regulation of the circadian clock genes. Gene network analysis identified two co-expression modules each associated with transpiration rate in cowpea and soybean, including a pair of negatively correlated modules between species. Module hub genes, including the ABA-degrading gene GmCYP707A4 and the trehalose-phosphatase/synthase gene VuTPS9 were identified. Inter-modular network analysis revealed putative co-players of the hub genes. Transgenic analyses verified the role of VuTPS9 in regulating transpiration rate under osmotic stresses. These findings propose that species-specific transcriptomic reprograming in leaves of the two crops suffering similar soil drought was not only a result of the different drought resistance level, but a cause of it.
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Affiliation(s)
- Pingping Fang
- College of Life Sciences, China Jiliang University, Xueyuan Street No.258, Hangzhou 310018, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Xueyuan Street No.258, Hangzhou 310018, China
| | - Arun Kumar Pandey
- College of Life Sciences, China Jiliang University, Xueyuan Street No.258, Hangzhou 310018, China
| | - Libo Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Xincun West Road No.255, Zibo 255000, China
| | - Xinyang Wu
- College of Life Sciences, China Jiliang University, Xueyuan Street No.258, Hangzhou 310018, China
| | - Yannan Hu
- College of Life Sciences, China Jiliang University, Xueyuan Street No.258, Hangzhou 310018, China
| | - Shiping Cheng
- Henan Provincial Key Lab of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Weilai Street No.1, Pingdingshan 467000, China
| | - Mingxuan Li
- College of Life Sciences, China Jiliang University, Xueyuan Street No.258, Hangzhou 310018, China
| | - Pei Xu
- Corresponding author. E-mail:
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Liang L, Zhang J, Xiao J, Li X, Xie Y, Tan H, Song X, Zhu L, Xue X, Xu L, Zhou P, Ran J, Sun B, Huang Z, Tang Y, Lin L, Sun G, Lai Y, Li H. Genome and pan-genome assembly of asparagus bean ( Vigna unguiculata ssp. sesquipedialis) reveal the genetic basis of cold adaptation. FRONTIERS IN PLANT SCIENCE 2022; 13:1059804. [PMID: 36589110 PMCID: PMC9802904 DOI: 10.3389/fpls.2022.1059804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Asparagus bean (Vigna unguiculata ssp. sesquipedialis) is an important cowpea subspecies. We assembled the genomes of Ningjiang 3 (NJ, 550.31 Mb) and Dubai bean (DB, 564.12 Mb) for comparative genomics analysis. The whole-genome duplication events of DB and NJ occurred at 64.55 and 64.81 Mya, respectively, while the divergence between soybean and Vigna occurred in the Paleogene period. NJ genes underwent positive selection and amplification in response to temperature and abiotic stress. In species-specific gene families, NJ is mainly enriched in response to abiotic stress, while DB is primarily enriched in respiration and photosynthesis. We established the pan-genomes of four accessions (NJ, DB, IT97K-499-35 and Xiabao II) and identified 20,336 (70.5%) core genes present in all the accessions, 6,507 (55.56%) variable genes in two individuals, and 2,004 (6.95%) unique genes. The final pan genome is 616.35 Mb, and the core genome is 399.78 Mb. The variable genes are manifested mainly in stress response functions, ABC transporters, seed storage, and dormancy control. In the pan-genome sequence variation analysis, genes affected by presence/absence variants were enriched in biological processes associated with defense responses, immune system processes, signal transduction, and agronomic traits. The results of the present study provide genetic data that could facilitate efficient asparagus bean genetic improvement, especially in producing cold-adapted asparagus bean.
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Affiliation(s)
- Le Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianwei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiachang Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaomei Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan, Chengdu, China
| | - Yongdong Xie
- Institute for Processing and Storage of Agricultural Products, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Huaqiang Tan
- Horticulture Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Xueping Song
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinru Xue
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linyu Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peihan Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianzhao Ran
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yi Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guochao Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunsun Lai
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huanxiu Li
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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Jiang L, Sun T, Wang X, Zong X, Wu C. Functional physiological phenotyping and transcriptome analysis provide new insight into strawberry growth and water consumption. FRONTIERS IN PLANT SCIENCE 2022; 13:1074132. [PMID: 36507431 PMCID: PMC9730707 DOI: 10.3389/fpls.2022.1074132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Global warming is expected to increase agricultural water scarcity; thus, optimized irrigation schedules are important and timely for sustainable crop production. Deficit irrigation, which balances crop growth and water consumption, has been proposed, but the critical threshold is not easily quantified. Here, we conducted experiments on strawberry plants subjecting progressive drought following various water recovery treatments on the high-throughput physiological phenotyping system "Plantarray". The critical soil water contents (θcri), below which the plant transpiration significantly decreased, were calculated from the inflection point of the transpiration rate (Tr) - volumetric soil water content (VWC) curve fitted by a piecewise function. The physiological traits of water relations were compared between the well-watered plants (CK), plants subjecting the treatment of rewatering at the point of θcri following progressive drought (WR_θcri), and the plants subjecting the treatment of rewatering at severe drought following progressive drought (WR_SD). The results showed that midday Tr, daily transpiration (E), and biomass gain of the plants under WR_θcri treatment were equivalent to CK during the whole course of the experiment, but those under WR_SD treatment were significantly lower than CK during the water stress phase that could not recover even after rehydration. To explore the gene regulatory mechanisms, transcriptome analysis of the samples collected 12 h before, 12 h post and 36 h post water recovery in the three treatments was conducted. GO and KEGG enrichment analyses for the differentially expressed genes indicated that genes involved in mineral absorption and flavonoid biosynthesis were among the most striking transcriptionally reversible genes under the WR_θcri treatment. Functional physiological phenotyping and transcriptome data provide new insight into a potential, quantitative, and balanceable water-saving strategy for strawberry irrigation and other agricultural crops.
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Affiliation(s)
- Lili Jiang
- Shandong Institute of Pomology, Taian, Shandong, China
| | - Ting Sun
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiaofang Wang
- Shandong Institute of Pomology, Taian, Shandong, China
| | - Xiaojuan Zong
- Shandong Institute of Pomology, Taian, Shandong, China
| | - Chong Wu
- Shandong Institute of Pomology, Taian, Shandong, China
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7
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Wu X, Fang P, Zhang P, Sun T, Wang X, Branca F, Xu P. Editorial: Improvement for Quality and Safety Traits in Horticultural Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:927779. [PMID: 35712592 PMCID: PMC9194942 DOI: 10.3389/fpls.2022.927779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Xinyang Wu
- College of Life Sciences, China Jiliang University, Hangzhou, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou, China
| | - Pingping Fang
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Peipei Zhang
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xinchao Wang
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - Ferdinando Branca
- Departments of Agriculture, Food, and Environment, University of Catania, Catania, Italy
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou, China
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Wu X, Sun T, Xu W, Sun Y, Wang B, Wang Y, Li Y, Wang J, Wu X, Lu Z, Xu P, Li G. Unraveling the Genetic Architecture of Two Complex, Stomata-Related Drought-Responsive Traits by High-Throughput Physiological Phenotyping and GWAS in Cowpea ( Vigna. Unguiculata L. Walp). Front Genet 2021; 12:743758. [PMID: 34777471 PMCID: PMC8581254 DOI: 10.3389/fgene.2021.743758] [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: 07/19/2021] [Accepted: 10/15/2021] [Indexed: 01/03/2023] Open
Abstract
Drought is one of the most devasting and frequent abiotic stresses in agriculture. While many morphological, biochemical and physiological indicators are being used to quantify plant drought responses, stomatal control, and hence the transpiration and photosynthesis regulation through it, is of particular importance in marking the plant capacity of balancing stress response and yield. Due to the difficulties in simultaneous, large-scale measurement of stomatal traits such as sensitivity and speed of stomatal closure under progressive soil drought, forward genetic mapping of these important behaviors has long been unavailable. The recent emerging phenomic technologies offer solutions to identify the water relations of whole plant and assay the stomatal regulation in a dynamic process at the population level. Here, we report high-throughput physiological phenotyping of water relations of 106 cowpea accessions under progressive drought stress, which, in combination of genome-wide association study (GWAS), enables genetic mapping of the complex, stomata-related drought responsive traits “critical soil water content” (θcri) and “slope of transpiration rate declining” (KTr). The 106 accessions showed large variations in θcri and KTr, indicating that they had broad spectrum of stomatal control in response to soil water deficit, which may confer them different levels of drought tolerance. Univariate GWAS identified six and fourteen significant SNPs associated with θcri and KTr, respectively. The detected SNPs distributed in nine chromosomes and accounted for 8.7–21% of the phenotypic variation, suggesting that both stomatal sensitivity to soil drought and the speed of stomatal closure to completion were controlled by multiple genes with moderate effects. Multivariate GWAS detected ten more significant SNPs in addition to confirming eight of the twenty SNPs as detected by univariate GWAS. Integrated, a final set of 30 significant SNPs associated with stomatal closure were reported. Taken together, our work, by combining phenomics and genetics, enables forward genetic mapping of the genetic architecture of stomatal traits related to drought tolerance, which not only provides a basis for molecular breeding of drought resistant cultivars of cowpea, but offers a new methodology to explore the genetic determinants of water budgeting in crops under stressful conditions in the phenomics era.
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Affiliation(s)
- Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Wenzhao Xu
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huaian, China
| | - Yudong Sun
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huaian, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanwei Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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9
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Zhang H, Xu W, Chen H, Chen J, Liu X, Chen X, Yang S. Transcriptomic analysis of salt tolerance-associated genes and diversity analysis using indel markers in yardlong bean (Vigna unguiculata ssp. sesquipedialis). BMC Genom Data 2021; 22:34. [PMID: 34530724 PMCID: PMC8447766 DOI: 10.1186/s12863-021-00989-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High salinity is a devastating abiotic stresses for crops. To understand the molecular basis of salinity stress in yardlong bean (Vigna unguiculata ssp. sesquipedalis), and to develop robust markers for improving this trait in germplasm, whole transcriptome RNA sequencing (RNA-seq) was conducted to compare the salt-tolerant variety Suzi 41 and salt-sensitive variety Sujiang 1419 under normal and salt stress conditions. RESULTS Compared with controls, 417 differentially expressed genes (DEGs) were identified under exposure to high salinity, including 42 up- and 11 down-regulated DEGs in salt-tolerant Suzi 41 and 186 up- and 197 down-regulated genes in salt-sensitive Sujiang 1419, validated by qRT-PCR. DEGs were enriched in "Glycolysis/Gluconeogenesis" (ko00010), "Cutin, suberine and wax biosynthesis" (ko00073), and "phenylpropanoid biosynthesis" (ko00940) in Sujiang 1419, although "cysteine/methionine metabolism" (ko00270) was the only pathway significantly enriched in salt-tolerant Suzi 41. Notably, AP2/ERF, LR48, WRKY, and bHLH family transcription factors (TFs) were up-regulated under high salt conditions. Genetic diversity analysis of 84 yardlong bean accessions using 26 InDel markers developed here could distinguish salt-tolerant and salt-sensitive varieties. CONCLUSIONS These findings show a limited set of DEGs, primarily TFs, respond to salinity stress in V. unguiculata, and that these InDels associated with salt-inducible loci are reliable for diversity analysis.
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Affiliation(s)
- Hongmei Zhang
- Soybean Research Institute of Nanjing Agricultural University/National Center for Soybean Improvement/National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, Jiangsu, China.,Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No. 50, Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Wenjing Xu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No. 50, Zhongling Street, Nanjing, 210014, Jiangsu, China.,College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No. 50, Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No. 50, Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Xiaoqing Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No. 50, Zhongling Street, Nanjing, 210014, Jiangsu, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, No. 50, Zhongling Street, Nanjing, 210014, Jiangsu, China.
| | - Shouping Yang
- Soybean Research Institute of Nanjing Agricultural University/National Center for Soybean Improvement/National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, Jiangsu, China.
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10
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Pandey AK, Jiang L, Moshelion M, Gosa SC, Sun T, Lin Q, Wu R, Xu P. Functional physiological phenotyping with functional mapping: A general framework to bridge the phenotype-genotype gap in plant physiology. iScience 2021; 24:102846. [PMID: 34381971 PMCID: PMC8333144 DOI: 10.1016/j.isci.2021.102846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/27/2021] [Accepted: 07/09/2021] [Indexed: 11/19/2022] Open
Abstract
The recent years have witnessed the emergence of high-throughput phenotyping techniques. In particular, these techniques can characterize a comprehensive landscape of physiological traits of plants responding to dynamic changes in the environment. These innovations, along with the next-generation genomic technologies, have brought plant science into the big-data era. However, a general framework that links multifaceted physiological traits to DNA variants is still lacking. Here, we developed a general framework that integrates functional physiological phenotyping (FPP) with functional mapping (FM). This integration, implemented with high-dimensional statistical reasoning, can aid in our understanding of how genotype is translated toward phenotype. As a demonstration of method, we implemented the transpiration and soil-plant-atmosphere measurements of a tomato introgression line population into the FPP-FM framework, facilitating the identification of quantitative trait loci (QTLs) that mediate the spatiotemporal change of transpiration rate and the test of how these QTLs control, through their interaction networks, phenotypic plasticity under drought stress.
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Affiliation(s)
- Arun K. Pandey
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100080, China
| | - Menachem Moshelion
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
- Corresponding author
| | - Sanbon Chaka Gosa
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Qin Lin
- Biozeron Biotechnology Co., Ltd, Shanghai 201800, China
| | - Rongling Wu
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA 17033, USA
- Corresponding author
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Corresponding author
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11
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Dhaliwal SK, Talukdar A, Gautam A, Sharma P, Sharma V, Kaushik P. Developments and Prospects in Imperative Underexploited Vegetable Legumes Breeding: A Review. Int J Mol Sci 2020; 21:E9615. [PMID: 33348635 PMCID: PMC7766301 DOI: 10.3390/ijms21249615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Vegetable legumes are an essential source of carbohydrates, vitamins, and minerals, along with health-promoting bioactive chemicals. The demand for the use of either fresh or processed vegetable legumes is continually expanding on account of the growing consumer awareness about their well-balanced diet. Therefore, sustaining optimum yields of vegetable legumes is extremely important. Here we seek to present d etails of prospects of underexploited vegetable legumes for food availability, accessibility, and improved livelihood utilization. So far research attention was mainly focused on pulse legumes' performance as compared to vegetable legumes. Wild and cultivated vegetable legumes vary morphologically across diverse habitats. This could make them less known, underutilized, and underexploited, and make them a promising potential nutritional source in developing nations where malnutrition still exists. Research efforts are required to promote underexploited vegetable legumes, for improving their use to feed the ever-increasing population in the future. In view of all the above points, here we have discussed underexploited vegetable legumes with tremendous potential; namely, vegetable pigeon pea (Cajanus cajan), cluster bean (Cyamopsis tetragonoloba), winged bean (Psophocarpus tetragonolobus), dolichos bean (Lablab purpureus), and cowpea (Vigna unguiculata), thereby covering the progress related to various aspects such as pre-breeding, molecular markers, quantitative trait locus (QTLs), genomics, and genetic engineering. Overall, this review has summarized the information related to advancements in the breeding of vegetable legumes which will ultimately help in ensuring food and nutritional security in developing nations.
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Affiliation(s)
- Sandeep Kaur Dhaliwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, India; (S.K.D.); (P.S.)
| | - Akshay Talukdar
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Ashish Gautam
- Department of Genetics and Plant Breeding, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145, India;
| | - Pankaj Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141004, India; (S.K.D.); (P.S.)
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India;
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
- Nagano University, Ueda 386-0031, Japan
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12
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Homem RV, dos Santos Joaquim A, Pimentel da Silva H, Mello Evangelista S, Komeroski MR, Doneda D, Rockett FC, de Oliveira Schmidt H, Rios A, Schäfer L, Rodrigues C, Kist T, de Oliveira V. Effect of Teff (Eragrostis tef) on Chemical and Technological Quality of Gluten-free Breads. JOURNAL OF CULINARY SCIENCE & TECHNOLOGY 2019. [DOI: 10.1080/15428052.2019.1679314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Raisa Vieira Homem
- Postgraduate Program in Food, Nutrition and Health, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | | | | | - Marina Rocha Komeroski
- Postgraduate Program in Food, Nutrition and Health, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Divair Doneda
- Nutrition Course, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fernanda Camboim Rockett
- Institute of Food Science and Technology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Helena de Oliveira Schmidt
- Institute of Food Science and Technology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Alessandro Rios
- Institute of Food Science and Technology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Laura Schäfer
- Institute of Biosciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Carlos Rodrigues
- Institute of Biosciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Tarso Kist
- Institute of Biosciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Viviani de Oliveira
- Postgraduate Program in Food, Nutrition and Health, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Nutrition Course, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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13
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Li G, Wu X, Hu Y, Muñoz-Amatriaín M, Luo J, Zhou W, Wang B, Wang Y, Wu X, Huang L, Lu Z, Xu P. Orphan genes are involved in drought adaptations and ecoclimatic-oriented selections in domesticated cowpea. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3101-3110. [PMID: 30949664 DOI: 10.1093/jxb/erz145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/20/2019] [Indexed: 05/19/2023]
Abstract
Orphan genes (OGs) are genes that are restricted to a single species or a particular taxonomic group. To date, little is known about the functions of OGs in domesticated crops. Here, we report our findings on the relationships between OGs and environmental adaptation in cowpea (Vigna unguiculata). We identified 578 expressed OGs, of which 73.2% were predicted to be non-coding. Transcriptomic analyses revealed a high rate of OGs that were drought inducible in roots when compared with conserved genes. Co-expression analysis further revealed the possible involvement of OGs in stress response pathways. Overexpression of UP12_8740, a drought-inducible OG, conferred enhanced tolerance to osmotic stresses and soil drought. By combining Capture-Seq and fluorescence-based Kompetitive allele-specific PCR (KASP), we efficiently genotyped single nucleotide polymorphisms (SNPs) on OGs across a 223 accession cowpea germplasm collection. Population genomic parameters, including polymorphism information content (PIC), expected heterozygosity (He), nucleotide diversity (π), and Tajima's D statistics, that were calculated based on these SNPs, showed distinct signatures between the grain- and vegetable-type subpopulations of cowpea. This study reinforces the idea that OGs are a valuable resource for identifying new genes related to species-specific environmental adaptations and fosters new insights that artificial selection on OGs might have contributed to balancing the adaptive and agronomic traits in domesticated crops in various ecoclimatic conditions.
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Affiliation(s)
- Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Lab Breeding Base for Sustainable Control of Plant Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaowen Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Maria Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Jie Luo
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wen Zhou
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lijuan Huang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pei Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Lab Breeding Base for Sustainable Control of Plant Pest and Disease, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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14
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Zegaoui Z, Planchais S, Cabassa C, Djebbar R, Belbachir OA, Carol P. Variation in relative water content, proline accumulation and stress gene expression in two cowpea landraces under drought. JOURNAL OF PLANT PHYSIOLOGY 2017; 218:26-34. [PMID: 28763706 DOI: 10.1016/j.jplph.2017.07.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 06/02/2017] [Accepted: 07/03/2017] [Indexed: 05/09/2023]
Abstract
Many landraces of cowpea [Vigna unguiculata (L.) Walp.] are adapted to particular geographical and climatic conditions. Here we describe two landraces grown respectively in arid and temperate areas of Algeria and assess their physiological and molecular responses to drought stress. As expected, when deprived of water cowpea plants lose water over time with a gradual reduction in transpiration rate. The landraces differed in their relative water content (RWC) and whole plant transpiration rate. The landrace from Menia, an arid area, retained more water in adult leaves. Both landraces responded to drought stress at the molecular level by increasing expression of stress-related genes in aerial parts, including proline metabolism genes. Expression of gene(s) encoding proline synthesis enzyme P5CS was up regulated and gene expression of ProDH, a proline catabolism enzyme, was down regulated. Relatively low amounts of proline accumulated in adult leaves with slight differences between the two landraces. During drought stress the most apical part of plants stayed relatively turgid with a high RWC compared to distal parts that wilted. Expression of key stress genes was higher and more proline accumulated at the apex than in distal leaves indicating that cowpea has a non-uniform stress response at the whole plant level. Our study reveals a developmental control of water stress through preferential proline accumulation in the upper tier of the cowpea plant. We also conclude that cowpea landraces display physiological adaptations to water stress suited to the arid and temperate climates in which they are cultivated.
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Affiliation(s)
- Zahia Zegaoui
- Sorbonne Universités, UPMC Univ Paris 06, iEES, UMR 7618, (UPEC, UPMC, CNRS, IRD, INRA, Paris Diderot), case 237, 4 place Jussieu, F-75252, Paris cedex 05, France; Laboratory of Biology and Physiology of Organisms, Faculty of Biological Sciences, Houari Boumediene University of Sciences and Technology, BP 32, El Alia 16111, Algeria
| | - Séverine Planchais
- Sorbonne Universités, UPMC Univ Paris 06, iEES, UMR 7618, (UPEC, UPMC, CNRS, IRD, INRA, Paris Diderot), case 237, 4 place Jussieu, F-75252, Paris cedex 05, France
| | - Cécile Cabassa
- Sorbonne Universités, UPMC Univ Paris 06, iEES, UMR 7618, (UPEC, UPMC, CNRS, IRD, INRA, Paris Diderot), case 237, 4 place Jussieu, F-75252, Paris cedex 05, France
| | - Reda Djebbar
- Laboratory of Biology and Physiology of Organisms, Faculty of Biological Sciences, Houari Boumediene University of Sciences and Technology, BP 32, El Alia 16111, Algeria
| | - Ouzna Abrous Belbachir
- Laboratory of Biology and Physiology of Organisms, Faculty of Biological Sciences, Houari Boumediene University of Sciences and Technology, BP 32, El Alia 16111, Algeria
| | - Pierre Carol
- Sorbonne Universités, UPMC Univ Paris 06, iEES, UMR 7618, (UPEC, UPMC, CNRS, IRD, INRA, Paris Diderot), case 237, 4 place Jussieu, F-75252, Paris cedex 05, France
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15
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Xu P, Wu X, Muñoz‐Amatriaín M, Wang B, Wu X, Hu Y, Huynh B, Close TJ, Roberts PA, Zhou W, Lu Z, Li G. Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (V. unguiculata L. Walp). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:547-557. [PMID: 27658053 PMCID: PMC5399003 DOI: 10.1111/pbi.12639] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/30/2016] [Accepted: 09/15/2016] [Indexed: 05/19/2023]
Abstract
Cowpea (V. unguiculata L. Walp) is a climate resilient legume crop important for food security. Cultivated cowpea (V. unguiculata L) generally comprises the bushy, short-podded grain cowpea dominant in Africa and the climbing, long-podded vegetable cowpea popular in Asia. How selection has contributed to the diversification of the two types of cowpea remains largely unknown. In the current study, a novel genotyping assay for over 50 000 SNPs was employed to delineate genomic regions governing pod length. Major, minor and epistatic QTLs were identified through QTL mapping. Seventy-two SNPs associated with pod length were detected by genome-wide association studies (GWAS). Population stratification analysis revealed subdivision among a cowpea germplasm collection consisting of 299 accessions, which is consistent with pod length groups. Genomic scan for selective signals suggested that domestication of vegetable cowpea was accompanied by selection of multiple traits including pod length, while the further improvement process was featured by selection of pod length primarily. Pod growth kinetics assay demonstrated that more durable cell proliferation rather than cell elongation or enlargement was the main reason for longer pods. Transcriptomic analysis suggested the involvement of sugar, gibberellin and nutritional signalling in regulation of pod length. This study establishes the basis for map-based cloning of pod length genes in cowpea and for marker-assisted selection of this trait in breeding programmes.
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Affiliation(s)
- Pei Xu
- Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouChina
- State Key Lab Breeding Base for Sustainable Control of Plant Pest and DiseaseZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Xinyi Wu
- Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouChina
| | - María Muñoz‐Amatriaín
- Department of Botany and Plant SciencesUniversity of California‐RiversideRiversideCAUSA
| | - Baogen Wang
- Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Xiaohua Wu
- Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Yaowen Hu
- Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Bao‐Lam Huynh
- Department of NematologyUniversity of California‐RiversideRiversideCAUSA
| | - Timothy J. Close
- Department of Botany and Plant SciencesUniversity of California‐RiversideRiversideCAUSA
| | - Philip A. Roberts
- Department of NematologyUniversity of California‐RiversideRiversideCAUSA
| | - Wen Zhou
- Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Zhongfu Lu
- Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouChina
| | - Guojing Li
- Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouChina
- State Key Lab Breeding Base for Sustainable Control of Plant Pest and DiseaseZhejiang Academy of Agricultural SciencesHangzhouChina
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