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Deng D, Sun S, Wu W, Duan C, Wu X, Zhu Z. Fine mapping and identification of a Fusarium wilt resistance gene FwS1 in pea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:171. [PMID: 38918246 DOI: 10.1007/s00122-024-04682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/20/2024] [Indexed: 06/27/2024]
Abstract
KEY MESSAGE A Fusarium wilt resistance gene FwS1 on pea chromosome 6 was identified and mapped to a 91.4 kb region by a comprehensive genomic-based approach, and the gene Psat6g003960 harboring NB-ARC domain was identified as the putative candidate gene. Pea Fusarium wilt, incited by Fusarium oxysporum f. sp. pisi (Fop), has always been a devastating disease that causes severe yield losses and economic damage in pea-growing regions worldwide. The utilization of pea cultivars carrying resistance gene is the most efficient approach for managing this disease. In order to finely map resistance gene, F2 populations were established through the cross between Shijiadacaiwan 1 (resistant) and Y4 (susceptible). The resistance genetic analysis indicated that the Fop resistance in Shijiadacaiwan 1 was governed by a single dominant gene, named FwS1. Based on the bulked segregant analysis sequencing analyses, the gene FwS1 was initially detected on chromosome 6 (i.e., linking group II, chr6LG2), and subsequent linkage mapping with 589 F2 individuals fine-mapped the gene FwS1 into a 91.4 kb region. The further functional annotation and haplotype analysis confirmed that the gene Psat6g003960, characterized by a NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) domain, was considered as the most promising candidate gene. The encoding amino acids were altered by a "T/C" single-nucleotide polymorphism (SNP) in the first exon of the Psat6g003960, and based on this SNP locus, the molecular marker A016180 was determined to be a diagnostic marker for FwS1 by validating its specificity in both pea accessions and genetic populations with different genetic backgrounds. The FwS1 with diagnostic KASP marker A016180 could facilitate marker-assisted selection in resistance pea breeding in pea. In addition, a comparison of the candidate gene Psat6g003960 in 74SN3B and SJ1 revealed the same sequences. This finding indicated that 74SN3B carried the candidate gene for FwS1, suggesting that FwS1 and Fwf may be closely linked or an identical resistant gene against Fusarium wilt.
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Affiliation(s)
- Dong Deng
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Suli Sun
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenqi Wu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Canxing Duan
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuehong Wu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Zhendong Zhu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Yang P, Bai Y, Zhao D, Cui J, Yang W, Gao Y, Zhang J, Wang Z, Wang M, Xue W, Chang J. Identification and functional marker development of SbPLSH1 conferring purple leaf sheath in sorghum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:137. [PMID: 38769163 DOI: 10.1007/s00122-024-04623-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/14/2024] [Indexed: 05/22/2024]
Abstract
KEY MESSAGE We identified a SbPLSH1gene conferring purple leaf sheath in sorghum (sorghumbicolor(L.) Moench)and developed a functional markerfor it. The purple leaf sheath of sorghum, a trait mostly related to anthocyanin deposition, is a visually distinguishable morphological marker widely used to evaluate the purity of crop hybrids. We aimed to dissect the genetic mechanism for leaf sheath color to mine the genes regulating this trait. In this study, two F2 populations were constructed by crossing a purple leaf sheath inbred line (Gaoliangzhe) with two green leaf sheath inbred lines (BTx623 and Silimei). Based on the results of bulked-segregant analysis sequencing, bulk-segregant RNA sequencing, and map-based cloning, SbPLSH1 (Sobic.006G175700), which encodes a bHLH transcription factor on chromosome 6, was identified as the candidate gene for purple leaf sheath in sorghum. Genetic analysis demonstrated that overexpression of SbPLSH1 in Arabidopsis resulted in anthocyanin deposition and purple petiole, while two single-nucleotide polymorphism (SNP) variants on the exon 6 resulted in loss of function. Further haplotype analysis revealed that there were two missense mutations and one cis-acting element mutation in SbPLSH1, which are closely associated with leaf sheath color in sorghum. Based on the variations, a functional marker (LSC4-2) for marker-assisted selection was developed, which has a broad-spectrum capability of distinguishing leaf sheath color in natural variants. In summary, this study lays a foundation for analyzing the genetic mechanism for sorghum leaf sheath color.
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Affiliation(s)
- Puyuan Yang
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Yuzhe Bai
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Dongting Zhao
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Weiping Yang
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Yukun Gao
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Jiandong Zhang
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Zhibo Wang
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Meng Wang
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China
| | - Wei Xue
- Baoding Vocational and Technical College, Baoding, 071000, China
| | - Jinhua Chang
- College of Agronomy, Hebei Agricultural University, Baoding, 071000, China.
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding, 071000, China.
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Wang Z, Lei Y, Liao B. Omics-driven advances in the understanding of regulatory landscape of peanut seed development. FRONTIERS IN PLANT SCIENCE 2024; 15:1393438. [PMID: 38766472 PMCID: PMC11099219 DOI: 10.3389/fpls.2024.1393438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Peanuts (Arachis hypogaea) are an essential oilseed crop known for their unique developmental process, characterized by aerial flowering followed by subterranean fruit development. This crop is polyploid, consisting of A and B subgenomes, which complicates its genetic analysis. The advent and progression of omics technologies-encompassing genomics, transcriptomics, proteomics, epigenomics, and metabolomics-have significantly advanced our understanding of peanut biology, particularly in the context of seed development and the regulation of seed-associated traits. Following the completion of the peanut reference genome, research has utilized omics data to elucidate the quantitative trait loci (QTL) associated with seed weight, oil content, protein content, fatty acid composition, sucrose content, and seed coat color as well as the regulatory mechanisms governing seed development. This review aims to summarize the advancements in peanut seed development regulation and trait analysis based on reference genome-guided omics studies. It provides an overview of the significant progress made in understanding the molecular basis of peanut seed development, offering insights into the complex genetic and epigenetic mechanisms that influence key agronomic traits. These studies highlight the significance of omics data in profoundly elucidating the regulatory mechanisms of peanut seed development. Furthermore, they lay a foundational basis for future research on trait-related functional genes, highlighting the pivotal role of comprehensive genomic analysis in advancing our understanding of plant biology.
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Affiliation(s)
- Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
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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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Li G, Guo X, Sun Y, Gangurde SS, Zhang K, Weng F, Wang G, Zhang H, Li A, Wang X, Zhao C. Physiological and biochemical mechanisms underlying the role of anthocyanin in acquired tolerance to salt stress in peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1368260. [PMID: 38529061 PMCID: PMC10961369 DOI: 10.3389/fpls.2024.1368260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/26/2024] [Indexed: 03/27/2024]
Abstract
Anthocyanin is an important pigment that prevents oxidative stress and mediates adaptation of plants to salt stress. Peanuts with dark red and black testa are rich in anthocyanin. However, correlation between salt tolerance and anthocyanin content in black and dark red testa peanuts is unknown. In this study, three peanut cultivars namely YZ9102 (pink testa), JHR1 (red testa) and JHB1 (black testa) were subjected to sodium chloride (NaCl) stress. The plant growth, ion uptake, anthocyanin accumulation, oxidation resistance and photosynthetic traits were comparatively analyzed. We observed that the plant height, leaf area and biomass under salt stress was highly inhibited in pink color testa (YZ9102) as compare to black color testa (JHB1). JHB1, a black testa colored peanut was identified as the most salt-tolerance cultivar, followed by red (JHR1) and pink(YZ9102). During salt stress, JHB1 exhibited significantly higher levels of anthocyanin and flavonoid accumulation compared to JHR1 and YZ9102, along with increased relative activities of antioxidant protection and photosynthetic efficiency. However, the K+/Na+ and Ca2+/Na+ were consistently decreased among three cultivars under salt stress, suggesting that the salt tolerance of black testa peanut may not be related to ion absorption. Therefore, we predicted that salt tolerance of JHB1 may be attributed to the accumulation of the anthocyanin and flavonoids, which activated antioxidant protection against the oxidative damage to maintain the higher photosynthetic efficiency and plant growth. These findings will be useful for improving salt tolerance of peanuts.
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Affiliation(s)
- Guanghui Li
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xin Guo
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanbin Sun
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
| | - Sunil S. Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Kun Zhang
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Fubin Weng
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Guanghao Wang
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
| | - Huan Zhang
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Aiqin Li
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xingjun Wang
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chuanzhi Zhao
- Shandong International Joint Laboratory of Agricultural Germplasm Resources Innovation, Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, China
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Raza A, Chen H, Zhang C, Zhuang Y, Sharif Y, Cai T, Yang Q, Soni P, Pandey MK, Varshney RK, Zhuang W. Designing future peanut: the power of genomics-assisted breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:66. [PMID: 38438591 DOI: 10.1007/s00122-024-04575-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 02/03/2024] [Indexed: 03/06/2024]
Abstract
KEY MESSAGE Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Yasir Sharif
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Pooja Soni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Manish K Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.
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Liu H, Zheng Z, Sun Z, Qi F, Wang J, Wang M, Dong W, Cui K, Zhao M, Wang X, Zhang M, Wu X, Wu Y, Luo D, Huang B, Zhang Z, Cao G, Zhang X. Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis. BMC Genomics 2024; 25:65. [PMID: 38229017 DOI: 10.1186/s12864-024-10005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/11/2024] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Pod shell thickness (PST) is an important agronomic trait of peanut because it affects the ability of shells to resist pest infestations and pathogen attacks, while also influencing the peanut shelling process. However, very few studies have explored the genetic basis of PST. RESULTS An F2 segregating population derived from a cross between the thick-shelled cultivar Yueyou 18 (YY18) and the thin-shelled cultivar Weihua 8 (WH8) was used to identify the quantitative trait loci (QTLs) for PST. On the basis of a bulked segregant analysis sequencing (BSA-seq), four QTLs were preliminarily mapped to chromosomes 3, 8, 13, and 18. Using the genome resequencing data of YY18 and WH8, 22 kompetitive allele-specific PCR (KASP) markers were designed for the genotyping of the F2 population. Two major QTLs (qPSTA08 and qPSTA18) were identified and finely mapped, with qPSTA08 detected on chromosome 8 (0.69-Mb physical genomic region) and qPSTA18 detected on chromosome 18 (0.15-Mb physical genomic region). Moreover, qPSTA08 and qPSTA18 explained 31.1-32.3% and 16.7-16.8% of the phenotypic variation, respectively. Fifteen genes were detected in the two candidate regions, including three genes with nonsynonymous mutations in the exon region. Two molecular markers (Tif2_A08_31713024 and Tif2_A18_7198124) that were developed for the two major QTL regions effectively distinguished between thick-shelled and thin-shelled materials. Subsequently, the two markers were validated in four F2:3 lines selected. CONCLUSIONS The QTLs identified and molecular markers developed in this study may lay the foundation for breeding cultivars with a shell thickness suitable for mechanized peanut shelling.
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Affiliation(s)
- Hongfei Liu
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450002, China
| | - Zheng Zheng
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450002, China
| | - Ziqi Sun
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Feiyan Qi
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Juan Wang
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Mengmeng Wang
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Kailu Cui
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Mingbo Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450002, China
| | - Xiao Wang
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Meng Zhang
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Xiaohui Wu
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450002, China
| | - Dandan Luo
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450002, China
| | - Bingyan Huang
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Zhongxin Zhang
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China
| | - Gangqiang Cao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450002, China.
| | - Xinyou Zhang
- Institute of Crop Molecular Breeding, The Shennong Laboraory, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Henan Provincial Key Laboratory for Oil Crops Improvement, Postgraduate T&R Base of Zhengzhou University, Henan Academy of Agricultural Sciences, Ministry of Agriculture, Zhengzhou, 450002, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450002, China.
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Liu M, Hu F, Liu L, Lu X, Li R, Wang J, Wu J, Ma L, Pu Y, Fang Y, Yang G, Wang W, Sun W. Physiological Analysis and Genetic Mapping of Short Hypocotyl Trait in Brassica napus L. Int J Mol Sci 2023; 24:15409. [PMID: 37895090 PMCID: PMC10607371 DOI: 10.3390/ijms242015409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Hypocotyl length is a botanical trait that affects the cold tolerance of Brassica napus L. (B. napus). In this study, we constructed an F2 segregating population using the cold-resistant short hypocotyl variety '16VHNTS158' and the cold-sensitive long hypocotyl variety 'Tianyou 2288' as the parents, and BSA-seq was employed to identify candidate genes for hypocotyl length in B. napus. The results of parental differences showed that the average hypocotyl lengths of '16VHNTS158' and 'Tianyou 2288' were 0.41 cm and 0.77 cm at the 5~6 leaf stage, respectively, after different low-temperature treatments, and '16VHNTS158' exhibited lower relative ion leakage rates compared to 'Tianyou 2288'. The contents of indole acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) in hypocotyls of '16VHNTS158' and 'Tianyou 2288' increased with decreasing temperatures, but the IAA and GA contents were significantly higher than those of 'Tianyou 2288', and the BR content was lower than that of 'Tianyou 2288'. The genetic analysis results indicate that the genetic model for hypocotyl length follows the 2MG-A model. By using SSR molecular markers, a QTL locus associated with hypocotyl length was identified on chromosome C04. The additive effect value of this locus was 0.025, and it accounted for 2.5% of the phenotypic variation. BSA-Seq further localized the major effect QTL locus on chromosome C04, associating it with 41 genomic regions. The total length of this region was 1.06 Mb. Within this region, a total of 20 non-synonymous mutation genes were identified between the parents, and 26 non-synonymous mutation genes were found within the pooled samples. In the reference genome of B. napus, this region was annotated with 24 candidate genes. These annotated genes are predominantly enriched in four pathways: DNA replication, nucleotide excision repair, plant hormone signal transduction, and mismatch repair. The findings of this study provide a theoretical basis for cloning genes related to hypocotyl length in winter rapeseed and their utilization in breeding.
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Affiliation(s)
| | | | - Lijun Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (M.L.)
| | | | | | | | | | | | | | | | | | | | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (M.L.)
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Yu B, Liu N, Huang L, Luo H, Zhou X, Lei Y, Yan L, Wang X, Chen W, Kang Y, Ding Y, Jin G, Pandey MK, Janila P, Kishan Sudini H, Varshney RK, Jiang H, Liu S, Liao B. Identification and application of a candidate gene AhAftr1 for aflatoxin production resistance in peanut seed (Arachis hypogaea L.). J Adv Res 2023:S2090-1232(23)00263-1. [PMID: 37739123 DOI: 10.1016/j.jare.2023.09.014] [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: 06/11/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
INTRODUCTION Peanut is susceptible to infection of Aspergillus fungi and conducive to aflatoxin contamination, hence developing aflatoxin-resistant variety is highly meaningful. Identifying functional genes or loci conferring aflatoxin resistance and molecular diagnostic marker are crucial for peanut breeding. OBJECTIVES This work aims to (1) identify candidate gene for aflatoxin production resistance, (2) reveal the related resistance mechanism, and (3) develop diagnostic marker for resistance breeding program. METHODS Resistance to aflatoxin production in a recombined inbred line (RIL) population derived from a high-yielding variety Xuhua13 crossed with an aflatoxin-resistant genotype Zhonghua 6 was evaluated under artificial inoculation for three consecutive years. Both genetic linkage analysis and QTL-seq were conducted for QTL mapping. The candidate gene was further fine-mapped using a secondary segregation mapping population and validated by transgenic experiments. RNA-Seq analysis among resistant and susceptible RILs was used to reveal the resistance pathway for the candidate genes. RESULTS The major effect QTL qAFTRA07.1 for aflatoxin production resistance was mapped to a 1.98 Mbp interval. A gene, AhAftr1 (Arachis hypogaea Aflatoxin resistance 1), was detected structure variation (SV) in leucine rich repeat (LRR) domain of its production, and involved in disease resistance response through the effector-triggered immunity (ETI) pathway. Transgenic plants with overexpression of AhAftr1(ZH6) exhibited 57.3% aflatoxin reduction compared to that of AhAftr1(XH13). A molecular diagnostic marker AFTR.Del.A07 was developed based on the SV. Thirty-six lines, with aflatoxin content decrease by over 77.67% compared to the susceptible control Zhonghua12 (ZH12), were identified from a panel of peanut germplasm accessions and breeding lines through using AFTR.Del.A07. CONCLUSION Our findings would provide insights of aflatoxin production resistance mechanisms and laid meaningful foundation for further breeding programs.
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Affiliation(s)
- Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yingbin Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Gaorui Jin
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Australia
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China.
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10
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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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11
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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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12
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Chen M, Li M, Zhao L, Song H. Deciphering evolutionary dynamics of WRKY genes in Arachis species. BMC Genomics 2023; 24:48. [PMID: 36707767 PMCID: PMC9881300 DOI: 10.1186/s12864-023-09149-z] [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: 12/11/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Cultivated peanut (Arachis hypogaea), a progeny of the cross between A. duranensis and A. ipaensis, is an important oil and protein crop from South America. To date, at least six Arachis genomes have been sequenced. WRKY transcription factors (TFs) play crucial roles in plant growth, development, and response to abiotic and biotic stresses. WRKY TFs have been identified in A. duranensis, A. ipaensis, and A. hypogaea cv. Tifrunner; however, variations in their number and evolutionary patterns across various Arachis spp. remain unclear. RESULTS WRKY TFs were identified and compared across different Arachis species, including A. duranensis, A. ipaensis, A. monticola, A. hypogaea cultivars (cv.) Fuhuasheng, A. hypogaea cv. Shitouqi, and A. hypogaea cv. Tifrunner. The results showed that the WRKY TFs underwent dynamic equilibrium between diploid and tetraploid peanut species, characterized by the loss of old WRKY TFs and retention of the new ones. Notably, cultivated peanuts inherited more conserved WRKY orthologs from wild tetraploid peanuts than their wild diploid donors. Analysis of the W-box elements and protein-protein interactions revealed that different domestication processes affected WRKY evolution across cultivated peanut varieties. WRKY TFs of A. hypogaea cv. Fuhuasheng and Shitouqi exhibited a similar domestication process, while those of cv. Tifrunner of the same species underwent a different domestication process based on protein-protein interaction analysis. CONCLUSIONS This study provides new insights into the evolution of WRKY TFs in Arachis spp.
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Affiliation(s)
- Mingwei Chen
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Meiran Li
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Longgang Zhao
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao, China
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13
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Ahmad N, Zhang K, Ma J, Yuan M, Zhao S, Wang M, Deng L, Ren L, Gangurde SS, Pan J, Ma C, Li C, Guo B, Wang X, Li A, Zhao C. Transcriptional networks orchestrating red and pink testa color in peanut. BMC PLANT BIOLOGY 2023; 23:44. [PMID: 36658483 PMCID: PMC9850581 DOI: 10.1186/s12870-023-04041-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 01/03/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND Testa color is an important trait of peanut (Arachis hypogaea L.) which is closely related with the nutritional and commercial value. Pink and red are main color of peanut testa. However, the genetic mechanism of testa color regulation in peanut is not fully understood. To elucidate a clear picture of peanut testa regulatory model, samples of pink cultivar (Y9102), red cultivar (ZH12), and two RNA pools (bulk red and bulk pink) constructed from F4 lines of Y9102 x ZH12 were compared through a bulk RNA-seq approach. RESULTS A total of 2992 differential expressed genes (DEGs) were identified among which 317 and 1334 were up-regulated and 225 and 1116 were down-regulated in the bulk red-vs-bulk pink RNA pools and Y9102-vs-ZH12, respectively. KEGG analysis indicates that these genes were divided into significantly enriched metabolic pathways including phenylpropanoid, flavonoid/anthocyanin, isoflavonoid and lignin biosynthetic pathways. Notably, the expression of the anthocyanin upstream regulatory genes PAL, CHS, and CHI was upregulated in pink and red testa peanuts, indicating that their regulation may occur before to the advent of testa pigmentation. However, the differential expression of down-stream regulatory genes including F3H, DFR, and ANS revealed that deepening of testa color not only depends on their gene expression bias, but also linked with FLS inhibition. In addition, the down-regulation of HCT, IFS, HID, 7-IOMT, and I2'H genes provided an alternative mechanism for promoting anthocyanin accumulation via perturbation of lignin and isoflavone pathways. Furthermore, the co-expression module of MYB, bHLH, and WRKY transcription factors also suggested a fascinating transcriptional activation complex, where MYB-bHLH could utilize WRKY as a co-option during the testa color regulation by augmenting anthocyanin biosynthesis in peanut. CONCLUSIONS These findings reveal candidate functional genes and potential strategies for the manipulation of anthocyanin biosynthesis to improve peanut varieties with desirable testa color.
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Affiliation(s)
- Naveed Ahmad
- 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, People's Republic of China
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kun Zhang
- 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, People's Republic of China
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, 250100, People's Republic of China
| | - Jing Ma
- 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, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Mei Yuan
- Shandong Peanut Research Institute, Qingdao, 266199, Shandong, People's Republic of 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, People's Republic of China
| | - Mingqing Wang
- Shandong Peanut Research Institute, Qingdao, 266199, Shandong, People's Republic of China
| | - Li Deng
- Kaifeng Academy of Agriculture and Forestry, Kaifeng, 475008, People's Republic of China
| | - Li Ren
- Kaifeng Academy of Agriculture and Forestry, Kaifeng, 475008, People's Republic of China
| | - Sunil S Gangurde
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - Jiaowen Pan
- 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, People's Republic of China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Changsheng 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, People's Republic of China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, 31793, USA
- Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA
| | - 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, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Aiqin 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, People's Republic of 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, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
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Wang X, Liu Y, Ouyang L, Yao R, He D, Han Z, Li W, Ding Y, Wang Z, Kang Y, Yan L, Chen Y, Huai D, Jiang H, Lei Y, Liao B. Metabolomics combined with transcriptomics analyses of mechanism regulating testa pigmentation in peanut. FRONTIERS IN PLANT SCIENCE 2022; 13:1065049. [PMID: 36589085 PMCID: PMC9800836 DOI: 10.3389/fpls.2022.1065049] [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: 10/09/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Peanut testa (seed coat) contains large amounts of flavonoids that significantly influence seed color, taste, and nutritional qualities. There are various colors of peanut testa, however, their precise flavonoid components and regulatory mechanism of pigmentation remain unclear. In this study, a total of 133 flavonoids were identified and absolutely quantified in the seed coat of four peanut cultivars with different testa color using a widely targeted metabolomic approach. Black peanut skin had more types and substantial higher levels of cyanidin-based anthocyanins, which possibly contribute to its testa coloration. Procyanidins and flavan-3-ols were the major co-pigmented flavonoids in the red, spot and black peanuts, while flavanols were the most abundant constitutes in white cultivar. Although the concentrations as well as composition characteristics varied, the content ratios of procyanidins to flavan-3-ols were similar in all samples except for white peanut. Furthermore, MYB-like transcription factors, anthocyanidin reductases (ANR), and UDP-glycosyltransferases (UGT) were found to be candidate genes involved in testa pigmentation via RNA-seq and weighted gene co-expression network analysis. It is proposed that UGTs and ANR compete for the substrate cyanidin and the prevalence of UGTs activities over ANR one will determine the color pattern of peanut testa. Our results provide a comprehensive report examining the absolute abundance of flavonoid profiles in peanut seed coat, and the finding are expected to be useful for further understanding of regulation mechanisms of seed coat pigmentation in peanut and other crops.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yue Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lei Ouyang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Ruonan Yao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhongkui Han
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weitao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yingbin Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Qi Y, Wang L, Li W, Xie Y, Zhao W, Dang Z, Li W, Zhao L, Zhang J. Phenotypic analysis of Longya-10 × pale flax hybrid progeny and identification of candidate genes regulating prostrate/erect growth in flax plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1044415. [PMID: 36561460 PMCID: PMC9763623 DOI: 10.3389/fpls.2022.1044415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Flax is a dual-purpose crop that is important for oil and fiber production. The growth habit is one of the crucial targets of selection during flax domestication. Wild hybridization between cultivated flax and wild flax can produce superior germplasms for flax breeding and facilitate the study of the genetic mechanism underlying agronomically important traits. In this study, we used pale flax, Linum grandiflorum, and L. perenne to pollinate Longya-10. Only pale flax interspecific hybrids were obtained, and the trait analysis of the F1 and F2 generations showed that the traits analyzed in this study exhibited disparate genetic characteristics. In the F1 generation, only one trait, i.e., the number of capsules per plant (140) showed significant heterosis, while the characteristics of other traits were closely associated with those of the parents or a decline in hybrid phenotypes. The traits of the F2 generation were widely separated, and the variation coefficient ranged from 9.96% to 146.15%. The quantitative trait locus underlying growth habit was preliminarily found to be situated on chromosome 2 through Bulked-segregant analysis sequencing. Then linkage mapping analysis was performed to fine-map GH2.1 to a 23.5-kb interval containing 4 genes. Among them, L.us.o.m.scaffold22.109 and L.us.o.m.scaffold22.112 contained nonsynonymous SNPs with Δindex=1. Combined with the qRT-PCR results, the two genes might be possible candidate genes for GH2.1. This study will contribute to the development of important germplasms for flax breeding, which would facilitate the elucidation of the genetic mechanisms regulating the growth habit and development of an ideal architecture for the flax plant.
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Liu T, Liu X, He J, Dong K, Pan W, Zhang L, Ren R, Zhang Z, Yang T. Identification and fine-mapping of a major QTL ( PH1.1) conferring plant height in broomcorn millet ( Panicum miliaceum). FRONTIERS IN PLANT SCIENCE 2022; 13:1010057. [PMID: 36304390 PMCID: PMC9593001 DOI: 10.3389/fpls.2022.1010057] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The plant height of broomcorn millet (Panicum miliaceum) is a significant agronomic trait that is closely related to its plant architecture, lodging resistance, and final yield. However, the genes underlying the regulation of plant height in broomcorn millet are rarely reported. Here, an F2 population derived from a cross between a normal variety, "Longmi12," and a dwarf mutant, "Zhang778," was constructed. Genetic analysis for the F2 and F2:3 populations revealed that the plant height was controlled by more than one locus. A major quantitative trait locus (QTL), PH1.1, was preliminarily identified in chromosome 1 using bulked segregant analysis sequencing (BSA-seq). PH1.1 was fine-mapped to a 109-kb genomic region with 15 genes using a high-density map. Among them, longmi011482 and longmi011489, containing nonsynonymous variations in their coding regions, and longmi011496, covering multiple insertion/deletion sequences in the promoter regions, may be possible candidate genes for PH1.1. Three diagnostic markers closely linked to PH1.1 were developed to validate the PH1.1 region in broomcorn millet germplasm. These findings laid the foundation for further understanding of the molecular mechanism of plant height regulation in broomcorn millet and are also beneficial to the breeding program for developing new varieties with optimal height.
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Affiliation(s)
- Tianpeng Liu
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xueying Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jihong He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Wanxiang Pan
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
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Zhang S, Chen J, Jiang T, Cai X, Wang H, Liu C, Tang L, Li X, Zhang X, Zhang J. Genetic mapping, transcriptomic sequencing and metabolic profiling indicated a glutathione S-transferase is responsible for the red-spot-petals in Gossypium arboreum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3443-3454. [PMID: 35986130 DOI: 10.1007/s00122-022-04191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
A GST for red-spot-petals in Gossypium arboreum was identified as the candidate under the scope of multi-omics approaches. Colored petal spots are correlated with insect pollination efficiency in Gossypium species. However, molecular mechanisms concerning the formation of red spots on Gossypium arboreum flowers remain elusive. In the current study, the Shixiya1-R (SxyR, with red spots) × Shixiya1-W (SxyW, without red spots) segregating population was utilized to determine that the red-spot-petal phenotype was levered by a single dominant locus. This phenotype was expectedly related to the anthocyanin metabolites, wherein the cyanidin and delphinidin derivatives constituted the major partition. Subsequently, this dominant locus was narrowed to a 3.27 Mb range on chromosome 7 by genomic resequencing from the two parents and the two segregated progeny bulks that have spotted petals or not. Furthermore, differential expressed genes generated from the two bulks at either of three sequential flower developmental stages that spanning the spot formation were intersected with the annotated ones that allocated to the 3.27 Mb interval, which returned eight genes. A glutathione S-transferase-coding gene (Gar07G08900) out of the eight was the only one that exhibited simultaneously differential expression among all three developmental stages, and it was therefore considered to be the probable candidate. Finally, functional validation upon this candidate was achieved by the appearance of scattered petal spots with inhibited expression of Gar07G08900. In conclusion, the current report identified a key gene for the red spotted petal in G. arboreum under the scope of multi-omics approaches, such efforts and embedded molecular resources would benefit future applications underlying the flower color trait in cotton.
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Affiliation(s)
- Sujun Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Jie Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Tao Jiang
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Xiao Cai
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Haitao Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Cunjing Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Liyuan Tang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Xinghe Li
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Xiangyun Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China.
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China.
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18
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Zhang K, Ma J, Gangurde SS, Hou L, Xia H, Li N, Pan J, Tian R, Huang H, Wang X, Zhang Y, Zhao C. Targeted metabolome analysis reveals accumulation of metabolites in testa of four peanut germplasms. FRONTIERS IN PLANT SCIENCE 2022; 13:992124. [PMID: 36186006 PMCID: PMC9523574 DOI: 10.3389/fpls.2022.992124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important source of edible oil and protein. Peanut testa (seed coat) provides protection for seeds and serves as a carrier for diversity metabolites necessary for human health. There is significant diversity available for testa color in peanut germplasms. However, the kinds and type of metabolites in peanut testa has not been comprehensively investigated. In this study, we performed metabolite profiling using UPLC-MS/MS for four peanut germplasm lines with different testa colors, including pink, purple, red, and white. A total of 85 metabolites were identified in four peanuts. Comparative metabolomics analysis identified 78 differentially accumulated metabolites (DAMs). Some metabolites showed significant correlation with other metabolites. For instance, proanthocyanidins were positively correlated with cyanidin 3-O-rutinoside and malvin, and negatively correlated with pelargonidin-3-glucoside. We observed that the total proanthocyanidins are most abundant in pink peanut variety WH10. The red testa accumulated more isoflavones, flavonols and anthocyanidins compared with that in pink testa. These results provided valuable information about differential accumulation of metabolites in testa with different color, which are helpful for further investigation of the molecular mechanism underlying biosynthesis and accumulation of these metabolites in peanut.
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Affiliation(s)
- Kun Zhang
- College of Tropical Crops, Hainan University, Haikou, China
- 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, China
- College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, China
| | - Jing Ma
- 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, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Sunil S. Gangurde
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - 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, China
- College of Life Sciences, Shandong Normal University, Jinan, 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, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Nana 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, China
| | - Jiaowen Pan
- 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, China
| | - Ruizheng Tian
- 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, China
| | - Huailing Huang
- 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, China
- College of Life Sciences, Shandong Normal University, Jinan, 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, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yindong Zhang
- College of Tropical Crops, Hainan University, Haikou, China
- Hainan Academy of Agricultural Sciences, Haikou, 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, China
- College of Life Sciences, Shandong Normal University, Jinan, China
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