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Zhang X, Zhang X, Wang L, Liu Q, Liang Y, Zhang J, Xue Y, Tian Y, Zhang H, Li N, Sheng C, Nie P, Feng S, Liao B, Bai D. Fine mapping of a QTL and identification of candidate genes associated with cold tolerance during germination in peanut ( Arachis hypogaea L.) on chromosome B09 using whole genome re-sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1153293. [PMID: 37223785 PMCID: PMC10200878 DOI: 10.3389/fpls.2023.1153293] [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: 01/29/2023] [Accepted: 03/28/2023] [Indexed: 05/25/2023]
Abstract
Low temperatures significantly affect the growth and yield of peanuts. Temperatures lower than 12 °C are generally detrimental for the germination of peanuts. To date, there has been no report on precise information on the quantitative trait loci (QTL) for cold tolerance during the germination in peanuts. In this study, we developed a recombinant inbred line (RIL) population comprising 807 RILs by tolerant and sensitive parents. Phenotypic frequencies of germination rate low-temperature conditions among RIL population showed normally distributed in five environments. Then, we constructed a high density SNP-based genetic linkage map through whole genome re-sequencing (WGRS) technique and identified a major quantitative trait locus (QTL), qRGRB09, on chromosome B09. The cold tolerance-related QTLs were repeatedly detected in all five environments, and the genetic distance was 6.01 cM (46.74 cM - 61.75 cM) after taking a union set. To further confirm that qRGRB09 was located on chromosome B09, we developed Kompetitive Allele Specific PCR (KASP) markers for the corresponding QTL regions. A regional QTL mapping analysis, which was conducted after taking the intersection of QTL intervals of all environments into account, confirmed that qRGRB09 was between the KASP markers, G22096 and G220967 (chrB09:155637831-155854093), and this region was 216.26 kb in size, wherein a total of 15 annotated genes were detected. This study illustrates the relevance of WGRS-based genetic maps for QTL mapping and KASP genotyping that facilitated QTL fine mapping of peanuts. The results of our study also provided useful information on the genetic architecture underlying cold tolerance during germination in peanuts, which in turn may be useful for those engaged in molecular studies as well as crop improvement in the cold-stressed environment.
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Affiliation(s)
- Xin Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
- State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Xiaoji Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Luhuan Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Qimei Liu
- College of Plant Protection, Shanxi Agricultural University, Taigu, China
| | - Yuying Liang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Jiayu Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Yunyun Xue
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Yuexia Tian
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Huiqi Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Na Li
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Cong Sheng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Pingping Nie
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Suping Feng
- College of Food Science and Engineering, Hainan Tropical Ocean College, Hainan, China
| | - Boshou Liao
- The 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
| | - Dongmei Bai
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
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Tong Z, Xu M, Zhang Q, Lin F, Fang D, Chen X, Zhu T, Liu Y, Xu H, Xiao B. Construction of a high-density genetic map and dissection of genetic architecture of six agronomic traits in tobacco ( Nicotiana tabacum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1126529. [PMID: 36875609 PMCID: PMC9975568 DOI: 10.3389/fpls.2023.1126529] [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: 12/18/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Tobacco (Nicotiana tabacum L.) is an economic crop and a model organism for studies on plant biology and genetics. A population of 271 recombinant inbred lines (RIL) derived from K326 and Y3, two elite flue-cured tobacco parents, has been constructed to investigate the genetic basis of agronomic traits in tobacco. Six agronomic traits including natural plant height (nPH), natural leaf number (nLN), stem girth (SG), inter-node length (IL), length of the largest leaf (LL) and width of the largest leaf (LW) were measured in seven environments, spanning the period between 2018 and 2021. We firstly developed an integrated SNP-indel-SSR linkage map with 43,301 SNPs, 2,086 indels and 937 SSRs, which contained 7,107 bin markers mapped on 24 LGs and covered 3334.88 cM with an average genetic distance of 0.469cM. Based on this high-density genetic map, a total of 70 novel QTLs were detected for six agronomic traits by a full QTL model using the software QTLNetwork, of which 32 QTLs showed significant additive effects, 18 QTLs showed significant additive-by-environment interaction effects, 17 pairs showed significant additive-by-additive epistatic effects and 13 pairs showed significant epistasis-by-environment interaction effects. In addition to additive effect as a major contributor to genetic variation, both epistasis effects and genotype-by-environment interaction effects played an important role in explaining phenotypic variation for each trait. In particular, qnLN6-1 was detected with considerably large main effect and high heritability ( h a 2 =34.80%). Finally, four genes including Nt16g00284.1, Nt16g00767.1, Nt16g00853.1, Nt16g00877.1 were predicted as pleiotropic candidate genes for five traits.
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Affiliation(s)
- Zhijun Tong
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Manling Xu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qixin Zhang
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Feng Lin
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dunhuang Fang
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Xuejun Chen
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
| | - Tianneng Zhu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yingchao Liu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haiming Xu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bingguang Xiao
- Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
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Yao Z, Zhang X, Liang Y, Zhang J, Xu Y, Chen S, Zhao D. NtCOMT1 responsible for phytomelatonin biosynthesis confers drought tolerance in Nicotiana tabacum. PHYTOCHEMISTRY 2022; 202:113306. [PMID: 35798089 DOI: 10.1016/j.phytochem.2022.113306] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Nicotiana tabacum (tobacco) is one of the most important industrial crops and its productivity is vulnerable to drought, particularly in Yunnan province, China due to the long water-deficit spring. Here, we aimed at identifying caffeic acid O-methyltransferase (COMT) in melatonin biosynthesis to provide genetic resources against drought tolerance of tobacco. The integration of the genome-wide identification, phylogenetic relationships, and conserved domain/motif analysis revealed that NtCOMT1 could be the probable functional COMT homolog for melatonin production. In vitro enzyme activity test approved that NtCOMT1 enabled the conversion of N-acetylserotonin into melatonin, occurring both in the cytoplasm and nucleus by subcellular localization analysis. The Km and Vmax values for NtCOMT1 at the optimum temperature (30 °C) were 266.0 μM and 2.155 nmol/min/mg protein. NtCOMT1 was significantly induced by drought stress; whereby if this gene functioned on promoting drought resistance was further conducted. Overexpression of NtCOMT1 resulted in decreased wilting in transgenic tobacco plants subjected to dehydration treatment. The combinatorial effects of NtCOMT1 in increasing melatonin content, inducing antioxidant system, and elevating the expression of drought-related genes could deliver the drought tolerance in tobacco. The characterization of NtCOMT1 may represent a solution to cope with the increasing drought stress in tobacco production in Yunnan province.
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Affiliation(s)
- Zhengping Yao
- Biocontrol Engineering Research Center of Plant Disease & Pest, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan University, Kunming, China; School of Life Science, Yunnan University, Kunming, China
| | - Xue Zhang
- Biocontrol Engineering Research Center of Plant Disease & Pest, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan University, Kunming, China; School of Life Science, Yunnan University, Kunming, China
| | - Yingchong Liang
- Biocontrol Engineering Research Center of Plant Disease & Pest, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan University, Kunming, China; School of Life Science, Yunnan University, Kunming, China
| | - Jiemei Zhang
- Biocontrol Engineering Research Center of Plant Disease & Pest, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan University, Kunming, China; School of Life Science, Yunnan University, Kunming, China
| | - Yi Xu
- Yunnan Institute of Materia Medica, Yunnan Baiyao Group Company Limited, Kunming, China
| | - Suiyun Chen
- Biocontrol Engineering Research Center of Plant Disease & Pest, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan University, Kunming, China; School of Ecology and Environmental Science, Yunnan University, Kunming, China.
| | - Dake Zhao
- Biocontrol Engineering Research Center of Plant Disease & Pest, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan University, Kunming, China; School of Ecology and Environmental Science, Yunnan University, Kunming, China.
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Zhang H, Zhang X, Li M, Yang Y, Li Z, Xu Y, Wang H, Wang D, Zhang Y, Wang H, Fu Q, Zheng J, Yi H. Molecular mapping for fruit-related traits, and joint identification of candidate genes and selective sweeps for seed size in melon. Genomics 2022; 114:110306. [DOI: 10.1016/j.ygeno.2022.110306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/22/2021] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
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Zhao J, Li H, Xu Y, Yin Y, Huang T, Zhang B, Wang Y, Li Y, Cao Y, An W. A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.). BMC PLANT BIOLOGY 2021; 21:350. [PMID: 34303361 PMCID: PMC8306383 DOI: 10.1186/s12870-021-03115-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/22/2021] [Indexed: 06/02/2023]
Abstract
BACKGROUND Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers. RESULTS In this study, two parental strains, 'Ningqi No. 1' (Lycium barbarum L.) and 'Yunnan Gouqi' (Lycium yunnanense Kuang et A.M. Lu), and 200 F1 hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis. CONCLUSIONS A chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.
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Affiliation(s)
- Jianhua Zhao
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd, Urumchi, 830022 China
| | - Yue Yin
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Ting Huang
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Bo Zhang
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Yajun Wang
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Yanlong Li
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Youlong Cao
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
| | - Wei An
- Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002 China
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Kumar P, Choudhary M, Jat BS, Kumar B, Singh V, Kumar V, Singla D, Rakshit S. Skim sequencing: an advanced NGS technology for crop improvement. J Genet 2021. [DOI: 10.1007/s12041-021-01285-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Zhang J, Yao Z, Zhang R, Mou Z, Yin H, Xu T, Zhao D, Chen S. Genome-Wide Identification and Expression Profile of the SNAT Gene Family in Tobacco ( Nicotiana tabacum). Front Genet 2020; 11:591984. [PMID: 33193735 PMCID: PMC7652900 DOI: 10.3389/fgene.2020.591984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/30/2020] [Indexed: 11/13/2022] Open
Abstract
Melatonin plays key roles in development and confers stress tolerance to plants. Serotonin N-acetyltransferase (SNAT) is either the enzyme involved in the last step or the penultimate enzyme of phytomelatonin biosynthesis. To date, SNAT genes have not been characterized in tobacco (Nicotiana tabacum), an economically important plant species. The sequence of the Acetyltransf_7 conserved domain was used as a query sequence, and 12 NtSNAT candidate genes were in turn identified in the genome of tobacco. These NtSNATs could be divided into two groups based on the phylogenetic tree. NtSNAT1 and NtSNAT2 clustered together with the other typical SNATs, but the other 10 NtSNATs separately clustered outside of the typical SNATs. These 10 NtSNATs have only motif 1, whereas representative SNATs, such as NtSNAT1 and NtSNAT2 or a SNAT from cyanobacteria, have five motifs. In addition, NtSNAT1 and NtSNAT2 are highly homologous to the characterized OsSNAT1, 62.95 and 71.36%, respectively; however, the homology between the other 10 NtSNAT genes and OsSNAT1 is low. Concomitantly, it is hypothesized that NtSNAT1 and NtSNAT2 are the homolog of SNATs, whereas the other 10 candidates could be considered NtSNAT-like genes. Furthermore, both Nicotiana tomentosiformis and Nicotiana sylvestris, two diploid ancestor species of N. tabacum, have two SNAT candidates; therefore, it is speculated that gene rearrangement or deletion during the process of genomic stabilization after whole-genome duplication or polyploidization led to the preservation of NtSNAT1 and NtSNAT2 during the evolution of tobacco from the ancestral diploid to the allotetraploid. NtSNAT and NtSNAT-like genes were differentially expressed in all organs under different stress conditions, indicating that these genes potentially associated with plant growth and development and stress resistance. Under different stress conditions, the expression of NtSNAT1 was significantly upregulated upon high-temperature and cadmium stresses, while the expression of NtSNAT2 did not significantly increase under any of the tested stress treatments. These results provide valuable information for elucidating the evolutionary relationship of SNAT genes in tobacco and genetic resources for improving tobacco production in the future.
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Affiliation(s)
- Jiemei Zhang
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China
| | - Zhengping Yao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China
| | - Renjun Zhang
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China.,School of Life Sciences, Yunnan University, Kunming, China
| | - Zongmin Mou
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China.,School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Honghui Yin
- Wenshan Branch of Yunnan Tobacco Company, Wenshan, China
| | - Tianyang Xu
- Wenshan Branch of Yunnan Tobacco Company, Wenshan, China
| | - Dake Zhao
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China.,School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Suiyun Chen
- Biocontrol Engineering Research Center of Plant Disease and Pest, Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China.,School of Ecology and Environmental Science, Yunnan University, Kunming, China
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