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Zhang X, Chen Z, Wang C, Zhou X, Tang N, Zhang W, Xu F, Yang Z, Luo C, Liao Y, Ye J. Genome-wide identification of HD-ZIP gene family and screening of genes related to prickle development in Zanthoxylum armatum. THE PLANT GENOME 2023; 16:e20295. [PMID: 36606521 DOI: 10.1002/tpg2.20295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/11/2022] [Indexed: 05/10/2023]
Abstract
Zanthoxylum armatum is an important cash crop for medicinal and food purposes in Asia. However, its stems and leaves are covered with a large number of prickles, which cause many problems in the production process. The homeodomain leucine zipper (HD-ZIP) gene family is a class of transcription factors unique to plants that play an important role in biological processes such as morphogenesis, signal transduction, and secondary metabolite synthesis. However, little is known about HD-ZIP gene information that may be involved in prickle development of Z. armatum. Here, we identified 76 ZaHDZ genes from the Z. armatum genome and classified them into four subfamilies (I-IV) based on phylogenetic analysis, a classification further supported by gene structure and conserved motif analysis. Seventy-six ZaHDZ genes were unevenly distributed on chromosomes. Evolutionary analysis revealed that the expansion of ZaHDZ genes mainly were due to whole-genome duplication (WGD) or segmental duplication, and they experienced strong purifying selection pressure in the process of evolution. A total of 47 cis-elements were identified in the promoter region of ZaHDZ genes. Quantitative real-time polymerase chain reaction analysis was performed on subfamily IV ZaHDZ gene expression levels in five tissues and under four hormone treatments. Finally, ZaHDZ16 was predicted to be the candidate gene most likely to be involved in prickle development of Z. armatum. These results contribute to a better understanding of the characteristics of HD-ZIP gene family and lay a foundation for further study on the function of genes related to prickle development of Z. armatum.
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Affiliation(s)
- Xiaoxi Zhang
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Zexiong Chen
- Research Institute for Special Plants, Chongqing Univ. of Arts and Sciences, Chongqing, 402160, China
| | - Caini Wang
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Xian Zhou
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Ning Tang
- Research Institute for Special Plants, Chongqing Univ. of Arts and Sciences, Chongqing, 402160, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
- Spice Crops Research Institute, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Zhiwu Yang
- Sichuan Academy of Forestry, Chengdu, Sichuan, 610081, China
| | - Chengrong Luo
- Sichuan Academy of Forestry, Chengdu, Sichuan, 610081, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
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Ro N, Haile M, Kim B, Cho GT, Lee J, Lee YJ, Hyun DY. Genome-Wide Association Study for Agro-Morphological Traits in Eggplant Core Collection. PLANTS (BASEL, SWITZERLAND) 2022; 11:2627. [PMID: 36235493 PMCID: PMC9571982 DOI: 10.3390/plants11192627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Eggplant is one of the most economically and nutritionally important vegetables worldwide. The study of the association of phenotypic traits with genetic factors is vital for the rapid and efficient identification and selection of eggplant genetic resources for breeding purposes with desired traits. The eggplant resources (587) collected from different countries, including Korea, were used for establishing the core collection. A total of 288 accessions were selected from 587 Solanum accessions based on 52 single nucleotide polymorphisms (SNPs) markers together with 17 morphological traits. This core collection was further used to analyze the genetic associations of eggplant morphological variations. A large variation was found among the evaluated eggplant accessions for some agro-morphological traits. Stem prickles and leaf prickles showed a significant positive correlation (r = 0.83***), followed by days to flowering and days to maturity (r = 0.64***). A total of 114,981 SNPs were filtered and used for phylogenetic tree analysis, population structure analysis, and genome-wide association study (GWAS). Among the agro-morphological traits, significantly associated SNPs were found for six traits. A total of 377 significantly associated SNPs with six agro-morphological traits were identified. These six traits and the number of SNPs were: days to maturity (51), flower size (121), fruit width (20), harvest fruit color (42), leaf prickles (38), and stem prickles (105). The largest fraction of significant SNPs (11.94%) was obtained on chromosome Ch01, followed by Ch07 and Ch06 with 11.67% and 10.08%, respectively. This study will help to develop markers linked to the most important agro-morphological traits of eggplant genetic resources and support the selection of desirable traits for eggplant breeding programs.
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Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Bichsaem Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Jungro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Yoon-Jung Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Do Yoon Hyun
- Department of Crops and Forestry, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea;
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Guan W, Ke C, Tang W, Jiang J, Xia J, Xie X, Yang M, Duan C, Wu W, Zheng Y. Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant. Int J Mol Sci 2022; 23:ijms231810258. [PMID: 36142175 PMCID: PMC9499331 DOI: 10.3390/ijms231810258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 02/08/2023] Open
Abstract
High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F2 plants from an interspecific cross (Solanum melongena × S. incanum) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F2:3 lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL.
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Affiliation(s)
- Wenxiang Guan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changjiao Ke
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiqi Tang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Jialong Jiang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Xia
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaofang Xie
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei Yang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chenfeng Duan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
| | - Yan Zheng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
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Qian Z, Ji Y, Li R, Lanteri S, Chen H, Li L, Jia Z, Cui Y. Identifying Quantitative Trait Loci for Thousand Grain Weight in Eggplant by Genome Re-Sequencing Analysis. Front Genet 2022; 13:841198. [PMID: 35664340 PMCID: PMC9157640 DOI: 10.3389/fgene.2022.841198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Eggplant (Solanum melongena L.; 2n = 24) is one of the most important Solanaceae vegetables and is primarily cultivated in China (approximately 42% of world production) and India (approximately 39%). Thousand-grain weight (TGW) is an important trait that affects eggplant breeding cost and variety promotion. This trait is controlled by quantitative trait loci (QTLs); however, no quantitative trait loci (QTL) has been reported for TGW in eggplant so far, and its potential genetic basis remain unclear. In this study, two eggplant lines, 17C01 (P1, wild resource, small seed) and 17C02 (P2, cultivar, large seed), were crossed to develop F1, F2 (308 lines), BC1P1 (44 lines), and BC1P2 (44 lines) populations for quantitative trait association analysis. The TGWs of P1, P2 and F1 were determined as 3.00, 3.98 and 3.77 g, respectively. The PG-ADI (polygene-controlled additive-dominance-epistasis) genetic model was identified as the optimal model for TGW and the polygene heritability value in the F2 generation was as high as 80.87%. A high-quality genetic linkage bin map was constructed with resequencing analysis. The map contained 3,918 recombination bins on 12 chromosomes, and the total length was 1,384.62 cM. A major QTL (named as TGW9.1) located on chromosome 9 was identified to be strongly associated with eggplant TGW, with a phenotypic variance explanation of 20.51%. A total of 45 annotated genes were identified in the genetic region of TGW9.1. Based on the annotation of Eggplant genome V3 and orthologous genes in Arabidopsis thaliana, one candidate gene SMEL_009g329850 (SmGTS1, encoding a putative ubiquitin ligase) contains 4 SNPs and 2 Indels consecutive intron mutations in the flank of the same exon in P1. SmGTS1 displayed significantly higher expression in P1 and was selected as a potential candidate gene controlling TGW in eggplant. The present results contribute to shed light on the genetic basis of the traits exploitable in future eggplant marker-assisted selection (MAS) breeding.
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Affiliation(s)
- Zongwei Qian
- National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Yanhai Ji
- National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Ranhong Li
- College of Life Sciences and Technology, Mudanjiang Normal University, Mudanjiang, China
| | - Sergio Lanteri
- DISAFA, Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Haili Chen
- National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Longfei Li
- Jingyan Yinong (Beijing) Seed Sci-Tech Co. Ltd., Beijing, China
| | - Zhiyang Jia
- Jingyan Yinong (Beijing) Seed Sci-Tech Co. Ltd., Beijing, China
| | - Yanling Cui
- National Engineering Research Center for Vegetables, Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
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