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Wang J, Wang E, Cheng S, Ma A. Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA. FRONTIERS IN PLANT SCIENCE 2024; 15:1361621. [PMID: 38504905 PMCID: PMC10948542 DOI: 10.3389/fpls.2024.1361621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/30/2024] [Indexed: 03/21/2024]
Abstract
Grain number per spike, a pivotal agronomic trait dictating wheat yield, lacks a comprehensive understanding of its underlying mechanism in Pubing3228, despite the identification of certain pertinent genes. Thus, our investigation sought to ascertain molecular markers and candidate regions associated with grain number per spike through a high-density genetic mapping approach that amalgamates site-specific amplified fragment sequencing (SLAF-seq) and bulked segregation analysis (BSA). To facilitate this, we conducted a comparative analysis of two wheat germplasms, Pubing3228 and Jing4839, known to exhibit marked discrepancies in spike shape. By leveraging this methodology, we successfully procured 2,810,474 SLAF tags, subsequently resulting in the identification of 187,489 single nucleotide polymorphisms (SNPs) between the parental strains. We subsequently employed the SNP-index association algorithm alongside the extended distribution (ED) association algorithm to detect regions associated with the trait. The former algorithm identified 24 trait-associated regions, whereas the latter yielded 70. Remarkably, the intersection of these two algorithms led to the identification of 25 trait-associated regions. Amongst these regions, we identified 399 annotated genes, including three genes harboring non-synonymous mutant SNP loci. Notably, the APETALA2 (AP2) transcription factor families, which exhibited a strong correlation with spike type, were also annotated. Given these findings, it is plausible to hypothesize that these genes play a critical role in determining spike shape. In summation, our study contributes significant insights into the genetic foundation of grain number per spike. The molecular markers and candidate regions we have identified can be readily employed for marker-assisted breeding endeavors, ultimately leading to the development of novel wheat cultivars possessing enhanced yield potential. Furthermore, conducting further functional analyses on the identified genes will undoubtedly facilitate a comprehensive elucidation of the underlying mechanisms governing spike development in wheat.
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Affiliation(s)
- Jiansheng Wang
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, Henan, China
- Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan, Henan, China
| | - Erwei Wang
- Pingdingshan Academy of Agricultural Science, Pingdingshan, Henan, China
| | - Shiping Cheng
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, Henan, China
- Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan, Henan, China
| | - Aichu Ma
- Pingdingshan Academy of Agricultural Science, Pingdingshan, Henan, China
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2
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Zhang H, Liu X, Zhou J, Strelkov SE, Fredua-Agyeman R, Zhang S, Li F, Li G, Wu J, Sun R, Hwang SF, Zhang S. Identification of Clubroot ( Plasmodiophora brassicae) Resistance Loci in Chinese Cabbage ( Brassica rapa ssp. pekinensis) with Recessive Character. Genes (Basel) 2024; 15:274. [PMID: 38540333 PMCID: PMC10970103 DOI: 10.3390/genes15030274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 06/15/2024] Open
Abstract
The soil-borne pathogen Plasmodiophora brassicae is the causal agent of clubroot, a major disease in Chinese cabbage (Brassica rapa ssp. pekinensis). The host's resistance genes often confer immunity to only specific pathotypes and may be rapidly overcome. Identification of novel clubroot resistance (CR) from germplasm sources is necessary. In this study, Bap246 was tested by being crossed with different highly susceptible B. rapa materials and showed recessive resistance to clubroot. An F2 population derived from Bap246 × Bac1344 was used to locate the resistance Quantitative Trait Loci (QTL) by Bulk Segregant Analysis Sequencing (BSA-Seq) and QTL mapping methods. Two QTL on chromosomes A01 (4.67-6.06 Mb) and A08 (10.42-11.43 Mb) were found and named Cr4Ba1.1 and Cr4Ba8.1, respectively. Fifteen and eleven SNP/InDel markers were used to narrow the target regions in the larger F2 population to 4.67-5.17 Mb (A01) and 10.70-10.84 Mb (A08), with 85 and 19 candidate genes, respectively. The phenotypic variation explained (PVE) of the two QTL were 30.97% and 8.65%, respectively. Combined with gene annotation, mutation site analysis, and real-time quantitative polymerase chain reaction (qRT-PCR) analysis, one candidate gene in A08 was identified, namely Bra020861. And an insertion and deletion (InDel) marker (co-segregated) named Crr1-196 was developed based on the gene sequence. Bra013275, Bra013299, Bra013336, Bra013339, Bra013341, and Bra013357 in A01 were the candidate genes that may confer clubroot resistance in Chinese cabbage. The resistance resource and the developed marker will be helpful in Brassica breeding programs.
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Affiliation(s)
- Hui Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
| | - Xitong Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
| | - Jinyan Zhou
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (S.E.S.); (R.F.-A.)
| | - Rudolph Fredua-Agyeman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (S.E.S.); (R.F.-A.)
| | - Shifan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
| | - Fei Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
| | - Guoliang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
| | - Rifei Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
| | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (S.E.S.); (R.F.-A.)
| | - Shujiang Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (H.Z.); (X.L.); (J.Z.); (S.Z.); (F.L.); (G.L.); (J.W.); (R.S.)
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3
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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Gong C, Wang Z, Li Z, Sun B, Luo W, Luo S, Chen S, Mai P, Li Z, Li Y, Wang Y, Li T. A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt. HORTICULTURE RESEARCH 2024; 11:uhad272. [PMID: 38333730 PMCID: PMC10852381 DOI: 10.1093/hr/uhad272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
Resistant crop cultivars can recruit beneficial rhizobacteria to resist disease. However, whether this recruitment is regulated by quantitative trait loci (QTL) is unclear. The role of QTL in recruiting specific bacteria against bacterial wilt (BW) is an important question of practical significance to disease management. Here, to identify QTL controlling BW resistance, Super-BSA was performed in F2 plants derived from resistant eggplant cultivar R06112 × susceptible cultivar S55193. The QTL was narrowed down through BC1F1-BC3F1 individuals by wilting symptoms and KASP markers. Rhizosphere bacterial composition of R06112, S55193, and resistant individuals EB158 (with the QTL) and susceptible individuals EB327 (without QTL) from BC2F1 generation were assessed by Illumina sequencing-based analysis, and the activation of plant immunity by the bacterial isolates was analyzed. Evidence showed that BW-resistant is controlled by one QTL located at the 270 kb region on chromosome 10, namely EBWR10, and nsLTPs as candidate genes confirmed by RNA-Seq. EBWR10 has a significant effect on rhizobacteria composition and significantly recruits Bacillus. pp. A SynCom of three isolated Bacillus. pp trains significantly reduced the disease incidence, changed activities of CAT, PPO, and PAL and concentration of NO, H2O2, and O2-, activated SA and JA signaling-dependent ISR, and displayed immune activation against Ralstonia solanacearum in eggplant. Our findings demonstrate for the first time that the QTL can recruit beneficial rhizobacteria, which jointly promote the suppression of BW. This method charts a path to develop the QTL in resistant cultivar-driven probiotics to ameliorate plant diseases.
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Affiliation(s)
- Chao Gong
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Zhenshuo Wang
- Department of Plant Pathology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhiliang Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Baojuan Sun
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Wenlong Luo
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Shanwei Luo
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Shuting Chen
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Peiting Mai
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Zhenxing Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
| | - Ye Li
- Harbin Academy of Agricultural Sciences, Harbin, Heilongjiang, 150029, China
| | - Yikui Wang
- Institute of Vegetable, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, 530007, China
| | - Tao Li
- Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangzhou, 510640, China
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5
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Vailleau F, Genin S. Ralstonia solanacearum: An Arsenal of Virulence Strategies and Prospects for Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:25-47. [PMID: 37506349 DOI: 10.1146/annurev-phyto-021622-104551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The group of strains constituting the Ralstonia solanacearum species complex (RSSC) is a prominent model for the study of plant-pathogenic bacteria because of its impact on agriculture, owing to its wide host range, worldwide distribution, and long persistence in the environment. RSSC strains have led to numerous studies aimed at deciphering the molecular bases of virulence, and many biological functions and mechanisms have been described to contribute to host infection and pathogenesis. In this review, we put into perspective recent advances in our understanding of virulence in RSSC strains, both in terms of the inventory of functions that participate in this process and their evolutionary dynamics. We also present the different strategies that have been developed to combat these pathogenic strains through biological control, antimicrobial agents, plant genetics, or microbiota engineering.
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Affiliation(s)
- Fabienne Vailleau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France; ,
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France; ,
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Sharma A, Gupta AK, Devi B. Current trends in management of bacterial pathogens infecting plants. Antonie Van Leeuwenhoek 2023; 116:303-326. [PMID: 36683073 DOI: 10.1007/s10482-023-01809-0] [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: 09/08/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023]
Abstract
Plants are continuously challenged by different pathogenic microbes that reduce the quality and quantity of produce and therefore pose a serious threat to food security. Among them bacterial pathogens are known to cause disease outbreaks with devastating economic losses in temperate, tropical and subtropical regions throughout the world. Bacteria are structurally simple prokaryotic microorganisms and are diverse from a metabolic standpoint. Bacterial infection process mainly involves successful attachment or penetration by using extracellular enzymes, type secretion systems, toxins, growth regulators and by exploiting different molecules that modulate plant defence resulting in successful colonization. Theses bacterial pathogens are extremely difficult to control as they develop resistance to antibiotics. Therefore, attempts are made to search for innovative methods of disease management by the targeting bacterial virulence and manipulating the genes in host plants by exploiting genome editing methods. Here, we review the recent developments in bacterial disease management including the bioactive antimicrobial compounds, bacteriophage therapy, quorum-quenching mediated control, nanoparticles and CRISPR/Cas based genome editing techniques for bacterial disease management. Future research should focus on implementation of smart delivery systems and consumer acceptance of these innovative methods for sustainable disease management.
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Affiliation(s)
- Aditi Sharma
- College of Horticulture and Forestry, Thunag- Mandi, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173 230, India.
| | - A K Gupta
- Department of Plant Pathology, Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173 230, India
| | - Banita Devi
- Department of Plant Pathology, Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173 230, India
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Zhang C, Xie W, Fu H, Chen Y, Chen H, Cai T, Yang Q, Zhuang Y, Zhong X, Chen K, Gao M, Liu F, Wan Y, Pandey MK, Varshney RK, Zhuang W. Whole genome resequencing identifies candidate genes and allelic diagnostic markers for resistance to Ralstonia solanacearum infection in cultivated peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2023; 13:1048168. [PMID: 36684803 PMCID: PMC9845939 DOI: 10.3389/fpls.2022.1048168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Bacterial wilt disease (BWD), caused by Ralstonia solanacearum is a major challenge for peanut production in China and significantly affects global peanut field productivity. It is imperative to identify genetic loci and putative genes controlling resistance to R. solanacearum (RRS). Therefore, a sequencing-based trait mapping approach termed "QTL-seq" was applied to a recombination inbred line population of 581 individuals from the cross of Yueyou 92 (resistant) and Xinhuixiaoli (susceptible). A total of 381,642 homozygous single nucleotide polymorphisms (SNPs) and 98,918 InDels were identified through whole genome resequencing of resistant and susceptible parents for RRS. Using QTL-seq analysis, a candidate genomic region comprising of 7.2 Mb (1.8-9.0 Mb) was identified on chromosome 12 which was found to be significantly associated with RRS based on combined Euclidean Distance (ED) and SNP-index methods. This candidate genomic region had 180 nonsynonymous SNPs and 14 InDels that affected 75 and 11 putative candidate genes, respectively. Finally, eight nucleotide binding site leucine rich repeat (NBS-LRR) putative resistant genes were identified as the important candidate genes with high confidence. Two diagnostic SNP markers were validated and revealed high phenotypic variation in the different resistant and susceptible RIL lines. These findings advocate the expediency of the QTL-seq approach for precise and rapid identification of candidate genomic regions, and the development of diagnostic markers that are applicable in breeding disease-resistant peanut varieties.
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Affiliation(s)
- Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Wenping Xie
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiwen Fu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuting Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhui Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Zhong
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kun Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meijia Gao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Institute of Oil Crops Research, Research Center for Genetics and Systems Biology of Leguminous Oil Plants, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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8
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Sharma A, Abrahamian P, Carvalho R, Choudhary M, Paret ML, Vallad GE, Jones JB. Future of Bacterial Disease Management in Crop Production. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:259-282. [PMID: 35790244 DOI: 10.1146/annurev-phyto-021621-121806] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial diseases are a constant threat to crop production globally. Current management strategies rely on an array of tactics, including improved cultural practices; application of bactericides, plant activators, and biocontrol agents; and use of resistant varieties when available. However, effective management remains a challenge, as the longevity of deployed tactics is threatened by constantly changing bacterial populations. Increased scrutiny of the impact of pesticides on human and environmental health underscores the need for alternative solutions that are durable, sustainable, accessible to farmers, and environmentally friendly. In this review, we discuss the strengths and shortcomings of existing practices and dissect recent advances that may shape the future of bacterial disease management. We conclude that disease resistance through genome modification may be the most effective arsenal against bacterial diseases. Nonetheless, more research is necessary for developing novel bacterial disease management tactics to meet the food demand of a growing global population.
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Affiliation(s)
- Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Peter Abrahamian
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
- Plant Pathogen Confirmatory Diagnostic Laboratory, USDA-APHIS, Beltsville, Maryland, USA
| | - Renato Carvalho
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Manoj Choudhary
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
| | - Mathews L Paret
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- North Florida Research and Education Center, University of Florida, Quincy, Florida, USA
| | - Gary E Vallad
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA;
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Ghosh S, Zhang S, Azam M, Agyenim-Boateng KG, Qi J, Feng Y, Li Y, Li J, Li B, Sun J. Identification of Genomic Loci and Candidate Genes Related to Seed Tocopherol Content in Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:1703. [PMID: 35807655 PMCID: PMC9269242 DOI: 10.3390/plants11131703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Soybean seeds are primary sources of natural tocopherols used by the food and pharmaceutical industries, owing to their beneficial impacts on human health. Selection for higher tocopherol contents in seeds along with other desirable traits is an important goal in soybean breeding. In order to identify the genomic loci and candidate genes controlling tocopherol content in soybean seeds, the bulked-segregant analysis technique was performed using a natural population of soybean consisting of 1525 accessions. We constructed the bulked-segregant analysis based on 98 soybean accessions that showed extreme phenotypic variation for the target trait, consisting of 49 accessions with extremely-high and 49 accessions with extremely-low tocopherol content. A total of 144 variant sites and 109 predicted genes related to tocopherol content were identified, in which a total of 83 genes were annotated by the gene ontology functions. Furthermore, 13 enriched terms (p < 0.05) were detected, with four of them found to be highly enriched: response to lipid, response to abscisic acid, transition metal ion transmembrane transporter activity, and double-stranded DNA binding. Especially, six candidate genes were detected at 41.8−41.9 Mb genomic hotspots on chromosome 5 based on ANNOtate VARiation analysis. Among the genes, only Glyma.05G243400 carried a non-synonymous mutation that encodes a “translation elongation factor EF1A or initiation factor IF2gamma family protein” was identified. The haplotype analysis confirmed that Glyma.05G243400 exhibited highly significant variations in terms of tocopherol content across multiple experimental locations, suggesting that it can be the key candidate gene regulating soybean seed tocopherols. The present findings provide novel gene resources related to seed tocopherols for further validation by genome editing, functional characterization, and genetic improvement targeting enhanced tocopherol composition in soybean molecular breeding.
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Affiliation(s)
- Suprio Ghosh
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
- Bangladesh Agricultural Research Institute, Gazipur 1701, Bangladesh
| | - Shengrui Zhang
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Muhammad Azam
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Kwadwo Gyapong Agyenim-Boateng
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Jie Qi
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Yue Feng
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Yecheng Li
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Jing Li
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Bin Li
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
| | - Junming Sun
- The National Engineering Research Center of Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.G.); (S.Z.); (M.A.); (K.G.A.-B.); (J.Q.); (Y.F.); (Y.L.); (J.L.)
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Lee S, Chakma N, Joung S, Lee JM, Lee J. QTL Mapping for Resistance to Bacterial Wilt Caused by Two Isolates of Ralstonia solanacearum in Chili Pepper (Capsicum annuum L.). PLANTS 2022; 11:plants11121551. [PMID: 35736702 PMCID: PMC9229654 DOI: 10.3390/plants11121551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
Bacterial wilt caused by the β-proteobacterium Ralstonia solanacearum is one of the most destructive soil-borne pathogens in peppers (Capsicum annuum L.) worldwide. Cultivated pepper fields in Korea face a continuous spread of this pathogen due to global warming. The most efficient and sustainable strategy for controlling bacterial wilt is to develop resistant pepper varieties. Resistance, which is quantitatively inherited, occurs differentially depending on R. solanacearum isolates. Therefore, in this study, we aimed to identify resistance quantitative trait loci (QTLs) in two F2 populations derived from self-pollination of a highly resistant pepper cultivar ‘Konesian hot’ using a moderately pathogenic ‘HS’ isolate and a highly pathogenic ‘HWA’ isolate of R. solanacearum for inoculation, via genotyping-by-sequencing analysis. QTL analysis revealed five QTLs, Bwr6w-7.2, Bwr6w-8.1, Bwr6w-9.1, Bwr6w-9.2, and Bwr6w-10.1, conferring resistance to the ‘HS’ isolate with R2 values of 13.05, 12.67, 15.07, 10.46, and 9.69%, respectively, and three QTLs, Bwr6w-5.1, Bwr6w-6.1, and Bwr6w-7.1, resistant to the ‘HWA’ isolate with phenotypic variances of 19.67, 16.50, and 12.56%, respectively. Additionally, six high-resolution melting (HRM) markers closely linked to the QTLs were developed. In all the markers, the mean disease index of the paternal genotype was significantly lower than that of the maternal genotype. The QTLs and HRM markers are expected to be useful for the development of pepper varieties with high resistance to bacterial wilt.
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Affiliation(s)
- Saeyoung Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Nidhi Chakma
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Sunjeong Joung
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Je Min Lee
- Department of Horticultural Science, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Korea;
| | - Jundae Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
- Correspondence: ; Tel.: +82-63-270-2560
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11
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Lozada DN, Bosland PW, Barchenger DW, Haghshenas-Jaryani M, Sanogo S, Walker S. Chile Pepper ( Capsicum) Breeding and Improvement in the "Multi-Omics" Era. FRONTIERS IN PLANT SCIENCE 2022; 13:879182. [PMID: 35592583 PMCID: PMC9113053 DOI: 10.3389/fpls.2022.879182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.
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Affiliation(s)
- Dennis N. Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | | | - Mahdi Haghshenas-Jaryani
- Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Stephanie Walker
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States
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Tanner F, Tonn S, de Wit J, Van den Ackerveken G, Berger B, Plett D. Sensor-based phenotyping of above-ground plant-pathogen interactions. PLANT METHODS 2022; 18:35. [PMID: 35313920 PMCID: PMC8935837 DOI: 10.1186/s13007-022-00853-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/08/2022] [Indexed: 05/20/2023]
Abstract
Plant pathogens cause yield losses in crops worldwide. Breeding for improved disease resistance and management by precision agriculture are two approaches to limit such yield losses. Both rely on detecting and quantifying signs and symptoms of plant disease. To achieve this, the field of plant phenotyping makes use of non-invasive sensor technology. Compared to invasive methods, this can offer improved throughput and allow for repeated measurements on living plants. Abiotic stress responses and yield components have been successfully measured with phenotyping technologies, whereas phenotyping methods for biotic stresses are less developed, despite the relevance of plant disease in crop production. The interactions between plants and pathogens can lead to a variety of signs (when the pathogen itself can be detected) and diverse symptoms (detectable responses of the plant). Here, we review the strengths and weaknesses of a broad range of sensor technologies that are being used for sensing of signs and symptoms on plant shoots, including monochrome, RGB, hyperspectral, fluorescence, chlorophyll fluorescence and thermal sensors, as well as Raman spectroscopy, X-ray computed tomography, and optical coherence tomography. We argue that choosing and combining appropriate sensors for each plant-pathosystem and measuring with sufficient spatial resolution can enable specific and accurate measurements of above-ground signs and symptoms of plant disease.
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Affiliation(s)
- Florian Tanner
- Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA Australia
| | - Sebastian Tonn
- Department of Biology, Plant-Microbe Interactions, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Jos de Wit
- Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Guido Van den Ackerveken
- Department of Biology, Plant-Microbe Interactions, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Bettina Berger
- Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA Australia
| | - Darren Plett
- Australian Plant Phenomics Facility, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA Australia
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13
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Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1355-1374. [PMID: 34931728 DOI: 10.1111/tpj.15646] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.
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Affiliation(s)
- Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
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14
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Du H, Yang J, Chen B, Zhang X, Xu X, Wen C, Geng S. Dual RNA-seq Reveals the Global Transcriptome Dynamics of Ralstonia solanacearum and Pepper ( Capsicum annuum) Hypocotyls During Bacterial Wilt Pathogenesis. PHYTOPATHOLOGY 2022; 112:630-642. [PMID: 34346759 DOI: 10.1094/phyto-01-21-0032-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial wilt, caused by Ralstonia solanacearum, is a serious disease in pepper. However, the interaction between the pathogen and pepper remains largely unknown. This study aimed to gain insights into determinants of pepper susceptibility and R. solanacearum pathogenesis. We assembled the complete genome of R. solanacearum strain Rs-SY1 and identified 5,106 predicted genes, including 84 type III effectors (T3E). RNA-seq was used to identify differentially expressed genes (DEGs) in susceptible pepper CM334 at 1 and 5 days postinoculation (dpi) with R. solanacearum. Dual RNA-seq was used to simultaneously capture transcriptome changes in the host and pathogen at 3 and 7 dpi. A total of 1,400, 3,335, 2,878, and 4,484 DEGs of pepper (PDEGs) were identified in the CM334 hypocotyls at 1, 3, 5, and 7 dpi, respectively. Functional enrichment of the PDEGs suggests that inducing ethylene production, suppression of photosynthesis, downregulation of polysaccharide metabolism, and weakening of cell wall defenses may contribute to successful infection by R. solanacearum. When comparing in planta and nutrient agar growth of the R. solanacearum, 218 and 1,042 DEGs of R. solanacearum (RDEGs) were detected at 3 and 7 dpi, respectively. Additional analysis of the RDEGs suggested that enhanced starch and sucrose metabolism, and upregulation of virulence factors may promote R. solanacearum colonization. Strikingly, 26 R. solanacearum genes were found to have similar DEG patterns during a variety of host-R. solanacearum interactions. This study provides a foundation for a better understanding of the transcriptional changes during pepper-R. solanacearum interactions and will aid in the discovery of potential susceptibility and virulence factors.
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Affiliation(s)
- Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Xiulan Xu
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- National Engineering Research Center for Vegetables, Beijing 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
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15
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QTL Mapping of Resistance to Bacterial Wilt in Pepper Plants (Capsicum annuum) Using Genotyping-by-Sequencing (GBS). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bacterial wilt (BW) disease, which is caused by Ralstonia solanacearum, is one globally prevalent plant disease leading to significant losses of crop production and yield with the involvement of a diverse variety of monocot and dicot host plants. In particular, the BW of the soil-borne disease seriously influences solanaceous crops, including peppers (sweet and chili peppers), paprika, tomatoes, potatoes, and eggplants. Recent studies have explored genetic regions that are associated with BW resistance for pepper crops. However, owing to the complexity of BW resistance, the identification of the genomic regions controlling BW resistance is poorly understood and still remains to be unraveled in the pepper cultivars. In this study, we performed the quantitative trait loci (QTL) analysis to identify genomic loci and alleles, which play a critical role in the resistance to BW in pepper plants. The disease symptoms and resistance levels for BW were assessed by inoculation with R. solanacearum. Genotyping-by-sequencing (GBS) was utilized in 94 F2 segregating populations originated from a cross between a resistant line, KC352, and a susceptible line, 14F6002-14. A total of 628,437 single-nucleotide polymorphism (SNP) was obtained, and a pepper genetic linkage map was constructed with putative 1550 SNP markers via the filtering criteria. The linkage map exhibited 16 linkage groups (LG) with a total linkage distance of 828.449 cM. Notably, QTL analysis with CIM (composite interval mapping) method uncovered pBWR-1 QTL underlying on chromosome 01 and explained 20.13 to 25.16% by R2 (proportion of explained phenotyphic variance by the QTL) values. These results will be valuable for developing SNP markers associated with BW-resistant QTLs as well as for developing elite BW-resistant cultivars in pepper breeding programs.
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Leaf-to-Whole Plant Spread Bioassay for Pepper and Ralstonia solanacearum Interaction Determines Inheritance of Resistance to Bacterial Wilt for Further Breeding. Int J Mol Sci 2021; 22:ijms22052279. [PMID: 33668965 PMCID: PMC7956186 DOI: 10.3390/ijms22052279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 01/27/2023] Open
Abstract
Bacterial wilt (BW) disease from Ralstonia solanacearum is a serious disease and causes severe yield losses in chili peppers worldwide. Resistant cultivar breeding is the most effective in controlling BW. Thus, a simple and reliable evaluation method is required to assess disease severity and to investigate the inheritance of resistance for further breeding programs. Here, we developed a reliable leaf-to-whole plant spread bioassay for evaluating BW disease and then, using this, determined the inheritance of resistance to R. solanacearum in peppers. Capsicum annuum ‘MC4′ displayed a completely resistant response with fewer disease symptoms, a low level of bacterial cell growth, and significant up-regulations of defense genes in infected leaves compared to those in susceptible ‘Subicho’. We also observed the spreading of wilt symptoms from the leaves to the whole susceptible plant, which denotes the normal BW wilt symptoms, similar to the drenching method. Through this, we optimized the evaluation method of the resistance to BW. Additionally, we performed genetic analysis for resistance inheritance. The parents, F1 and 90 F2 progenies, were evaluated, and the two major complementary genes involved in the BW resistance trait were confirmed. These could provide an accurate evaluation to improve resistant pepper breeding efficiency against BW.
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17
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Chromosomal Distribution of Genes Conferring Tolerance to Abiotic Stresses Versus That of Genes Controlling Resistance to Biotic Stresses in Plants. Int J Mol Sci 2020; 21:ijms21051820. [PMID: 32155784 PMCID: PMC7084258 DOI: 10.3390/ijms21051820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 12/18/2022] Open
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