1
|
Achilonu CC, Gryzenhout M, Marais GJ, Madisha MT, Ghosh S. Random amplified microsatellites (RAMS) analysis ascertains genetic variation of Alternaria alternata causing black spot disease on Carya illinoinensis in South Africa. Front Genet 2023; 14:1213102. [PMID: 37842646 PMCID: PMC10569608 DOI: 10.3389/fgene.2023.1213102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Limited information regarding the occurrence of black spot disease of pecan (Carya illinoinensis), caused by A. alternata, in South Africa is known. The pecan industry is growing rapidly, so it is essential to understand the impact of the fungal pathogen to pecan health. In this study, the genetic variation of 364 A. alternata isolates was investigated by two RAMS primers (CCA5 and CGA5). In total, 6,525 alleles were produced, with a minimum of 3,182 alleles on the CGA5 primer and maximum of 3,343 alleles for CCA5 primer. Further analysis of the primers showed relatively low genetic diversity of A. alternata isolate populations, with mean values; (H = 0.12) and Shannon's information index (I = 0.20). The analysis of molecular variance (AMOVA) revealed significant differences between populations, with 88% of the genetic variation was found within populations (Nm = 3.59, PhiPT = 0.12), and were not significantly different (p > 0.001). While 12% variation was observed among populations (Nm = 2.89, PhiPT = 0.08) and the estimates were statistically significant (p < 0.001). STRUCTURE HARVESTER output showed that K value is K = 8, where ΔK cannot find the true number of populations because of less variation. The dendrogram cluster tree generated by Ward's analysis unveiled two main distinct clades and 10 sub-clades, revealing similar findings as those of PCoA analysis clusters. Therefore, it was evident that these analyses depicted no distinct relationship between the A. alternata isolates and their geographic locations or the prevalence of distribution among the populations.
Collapse
Affiliation(s)
- Conrad Chibunna Achilonu
- Department of Plant Sciences, Division of Plant Pathology, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Marieka Gryzenhout
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Gert Johannes Marais
- Department of Plant Sciences, Division of Plant Pathology, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | | | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| |
Collapse
|
2
|
Nishio S, Moriya S, Kunihisa M, Takeuchi Y, Imai A, Takada N. Rapid and easy construction of a simplified amplicon sequencing (simplified AmpSeq) library for marker-assisted selection. Sci Rep 2023; 13:10575. [PMID: 37386134 PMCID: PMC10310812 DOI: 10.1038/s41598-023-37522-1] [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: 05/10/2023] [Accepted: 06/22/2023] [Indexed: 07/01/2023] Open
Abstract
Marker-assisted selection (MAS) is fundamental for plant breeding programs, as it can identify desirable seedlings at a young stage and reduce the cost, time and space needed for plant maintenance, especially for perennial crops. To facilitate the process of genotyping, which is time consuming and laborious, we developed a simplified amplicon sequencing (simplified AmpSeq) library construction method for next-generation sequencing that can be applied to MAS in breeding programs. The method is based on one-step PCR with a mixture of two primer sets: the first consisting of tailed target primers, the second of primers that contain flow-cell binding sites, indexes and tail sequences complementary to those in the first set. To demonstrate the process of MAS using s implified AmpSeq, we created databases of genotypes for important traits by using cultivar collections including triploid cultivars and segregating seedlings of Japanese pear (Pyrus pyrifolia Nakai), Japanese chestnut (Castanea crenata Sieb. et Zucc.) and apple (Malus domestica Borkh.). Simplified AmpSeq has the advantages of high repeatability, ability to estimate allele number in polyploid species and semi-automatic evaluation using target allele frequencies. Because this method provides high flexibility for designing primer sets and targeting any variant, it will be useful for plant breeding programs.
Collapse
Affiliation(s)
- Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan.
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, Morioka, Iwate, 020-0123, Japan
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Yukie Takeuchi
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Atsushi Imai
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Norio Takada
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| |
Collapse
|
3
|
Khan A, Korban SS. Breeding and genetics of disease resistance in temperate fruit trees: challenges and new opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3961-3985. [PMID: 35441862 DOI: 10.1007/s00122-022-04093-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Climate change, large monocultures of disease-susceptible cultivars, overuse of pesticides, and the emergence of new pathogens or pathogenic strains causing economic losses are all major threats to our environment, health, food, and nutritional supply. Temperate tree fruit crops belonging to the Rosaceae family are the most economically important and widely grown fruit crops. These long-lived crops are under attack from many different pathogens, incurring major economic losses. Multiple chemical sprays to control various diseases annually is a common practice, resulting in significant input costs, as well as environmental and health concerns. Breeding for disease resistance has been undertaken primarily in pome fruit crops (apples and pears) for a few fungal and bacterial diseases, and to a lesser extent in some stone fruit crops. These breeding efforts have taken multiple decades due to the biological constraints and complex genetics of these tree fruit crops. Over the past couple of decades, major advances have been made in genetic and physical mapping, genomics, biotechnology, genome sequencing, and phenomics, along with accumulation of large germplasm collections in repositories. These valuable resources offer opportunities to make significant advances in greatly reducing the time needed to either develop new cultivars or modify existing economic cultivars for enhanced resistance to multiple diseases. This review will cover current knowledge, challenges, and opportunities in breeding for disease resistance in temperate tree fruit crops.
Collapse
Affiliation(s)
- Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA.
| | - Schuyler S Korban
- Department of Natural Sciences and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
4
|
Li J, Zhang M, Li X, Khan A, Kumar S, Allan AC, Lin-Wang K, Espley RV, Wang C, Wang R, Xue C, Yao G, Qin M, Sun M, Tegtmeier R, Liu H, Wei W, Ming M, Zhang S, Zhao K, Song B, Ni J, An J, Korban SS, Wu J. Pear genetics: Recent advances, new prospects, and a roadmap for the future. HORTICULTURE RESEARCH 2022; 9:uhab040. [PMID: 35031796 PMCID: PMC8778596 DOI: 10.1093/hr/uhab040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/14/2023]
Abstract
Pear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for "pear-omics".
Collapse
Affiliation(s)
- Jiaming Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyue Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Xiaolong Li
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Awais Khan
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Satish Kumar
- Hawke’s Bay Research Centre, The New Zealand Institute for Plant and Food Research Limited, Havelock North 4157, New Zealand
| | - Andrew Charles Allan
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Kui Lin-Wang
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Richard Victor Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Caihong Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Runze Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Cheng Xue
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Gaifang Yao
- School of Food and Biological Engineering, Hefei University of Technology, 230009 Hefei, China
| | - Mengfan Qin
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Manyi Sun
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Richard Tegtmeier
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456, USA
| | - Hainan Liu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Weilin Wei
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Meiling Ming
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Shaoling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kejiao Zhao
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Bobo Song
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiangping Ni
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianping An
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong 271018, China
| | - Schuyler S Korban
- Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jun Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
5
|
Nishio S, Hayashi T, Shirasawa K, Saito T, Terakami S, Takada N, Takeuchi Y, Moriya S, Itai A. Genome-wide association study of individual sugar content in fruit of Japanese pear (Pyrus spp.). BMC PLANT BIOLOGY 2021; 21:378. [PMID: 34399685 PMCID: PMC8369641 DOI: 10.1186/s12870-021-03130-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Understanding mechanisms of sugar accumulation and composition is essential to determining fruit quality and maintaining a desirable balance of sugars in plant storage organs. The major sugars in mature Rosaceae fruits are sucrose, fructose, glucose, and sorbitol. Among these, sucrose and fructose have high sweetness, whereas glucose and sorbitol have low sweetness. Japanese pear has extensive variation in individual sugar contents in mature fruit. Increasing total sugar content and that of individual high-sweetness sugars is a major target of breeding programs. The objective of this study was to identify quantitative trait loci (QTLs) associated with fruit traits including individual sugar accumulation, to infer the candidate genes underlying the QTLs, and to assess the potential of genomic selection for breeding pear fruit traits. RESULTS We evaluated 10 fruit traits and conducted genome-wide association studies (GWAS) for 106 cultivars and 17 breeding populations (1112 F1 individuals) using 3484 tag single-nucleotide polymorphisms (SNPs). By implementing a mixed linear model and a Bayesian multiple-QTL model in GWAS, 56 SNPs associated with fruit traits were identified. In particular, a SNP located close to acid invertase gene PPAIV3 on chromosome 7 and a newly identified SNP on chromosome 11 had quite large effects on accumulation of sucrose and glucose, respectively. We used 'Golden Delicious' doubled haploid 13 (GDDH13), an apple reference genome, to infer the candidate genes for the identified SNPs. In the region flanking the SNP on chromosome 11, there is a tandem repeat of early responsive to dehydration (ERD6)-like sugar transporter genes that might play a role in the phenotypes observed. CONCLUSIONS SNPs associated with individual sugar accumulation were newly identified at several loci, and candidate genes underlying QTLs were inferred using advanced apple genome information. The candidate genes for the QTLs are conserved across Pyrinae genomes, which will be useful for further fruit quality studies in Rosaceae. The accuracies of genomic selection for sucrose, fructose, and glucose with genomic best linear unbiased prediction (GBLUP) were relatively high (0.67-0.75), suggesting that it would be possible to select individuals having high-sweetness fruit with high sucrose and fructose contents and low glucose content.
Collapse
Affiliation(s)
- Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO (NIFTS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Takeshi Hayashi
- Research Center for Agricultural Information Technology, NARO, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666 Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 Japan
| | - Toshihiro Saito
- Institute of Fruit Tree and Tea Science, NARO (NIFTS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Shingo Terakami
- Institute of Fruit Tree and Tea Science, NARO (NIFTS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Norio Takada
- Institute of Fruit Tree and Tea Science, NARO (NIFTS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Yukie Takeuchi
- Institute of Fruit Tree and Tea Science, NARO (NIFTS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605 Japan
| | - Shigeki Moriya
- Institute of Fruit Tree and Tea Science, NARO, Morioka, Iwate 020-0123 Japan
| | - Akihiko Itai
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Kitainayazuma, Seika, Kyoto 619-0244 Japan
| |
Collapse
|
6
|
Terakami S, Adachi Y, Takeuchi Y, Takada N, Nishio S, Saito T, Yamamoto T. Development of an SSR marker set for efficient selection for resistance to black spot disease in pear breeding. BREEDING SCIENCE 2021; 71:240-252. [PMID: 34377072 PMCID: PMC8329887 DOI: 10.1270/jsbbs.20136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/24/2020] [Indexed: 06/13/2023]
Abstract
Black spot disease, which is caused by Alternaria alternata (Fries) Keissler Japanese pear pathotype, is one of the most harmful diseases in Japanese pear cultivation. Because of the potential harm of fungicides to consumers and the environment, resistant cultivars are desired. In this study, to enable efficient marker-assisted selection in pear breeding, we conducted comprehensive inoculation tests and genotyping with 207 pear cultivars. We identified a marker set (Mdo.chr11.27 and Mdo.chr11.34) suitable for selection for black spot resistance. In most susceptible cultivars, Mdo.chr11.27 amplified a 220-bp band and Mdo.chr11.34 amplified a 259-bp band. The genotype of Mdo.chr11.34 corresponds perfectly to the estimated genotype of Japanese pears susceptible to black spot disease. Using linkage analysis, we identified the positions of the gene for susceptibility to black spot disease in Chinese pear. Mdo.chr11.27 and Mdo.chr11.34 were tightly linked to susceptibility in Chinese pear, and the susceptibility gene was mapped at the top of linkage group 11, similar to that in Japanese pear. This marker set and the accumulation of phenotypic data will enable efficient marker-assisted breeding for black spot resistance in pear breeding.
Collapse
Affiliation(s)
- Shingo Terakami
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Yoshihiko Adachi
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Yukie Takeuchi
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Norio Takada
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Toshihiro Saito
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan
| |
Collapse
|
7
|
Sun M, Zhang M, Singh J, Song B, Tang Z, Liu Y, Wang R, Qin M, Li J, Khan A, Wu J. Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears. BMC Genomics 2020; 21:809. [PMID: 33213380 PMCID: PMC7678159 DOI: 10.1186/s12864-020-07226-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri ('Dangshansuli', an Asian pear) and Pyrus communis ('Bartlett', a European pear) genomes, but the patterns of genetic variation and selection pressure on these genes during pear domestication have remained unsolved. RESULTS In this study, 338 and 412 NBS-encoding genes were identified from Asian and European pear genomes. This difference between the two pear species was the result of proximal duplications. About 15.79% orthologous gene pairs had Ka/Ks ratio more than one, indicating two pear species undergo strong positive selection after the divergence of Asian and European pear. We identified 21 and 15 NBS-encoding genes under fire blight and black spot disease-related QTL, respectively, suggesting their importance in disease resistance. Domestication caused decreased nucleotide diversity across NBS genes in Asian cultivars (cultivated 6.23E-03; wild 6.47E-03), but opposite trend (cultivated 6.48E-03; wild 5.91E-03) appeared in European pears. Many NBS-encoding coding regions showed Ka/Ks ratio of greater than 1, indicating the role of positive selection in shaping diversity of NBS-encoding genes in pear. Furthermore, we detected 295 and 122 significantly different SNPs between wild and domesticated accessions in Asian and European pear populations. Two NBS genes (Pbr025269.1 and Pbr019876.1) with significantly different SNPs showed >5x upregulation between wild and cultivated pear accessions, and > 2x upregulation in Pyrus calleryana after inoculation with Alternaria alternata. We propose that positively selected and significantly different SNPs of an NBS-encoding gene (Pbr025269.1) regulate gene expression differences in the wild and cultivated groups, which may affect resistance in pear against A. alternata. CONCLUSION Proximal duplication mainly led to the different number of NBS-encoding genes in P. bretschneideri and P. communis genomes. The patterns of genetic diversity and positive selection pressure differed between Asian and European pear populations, most likely due to their independent domestication events. This analysis helps us understand the evolution, diversity, and selection pressure in the NBS-encoding gene family in Asian and European populations, and provides opportunities to study mechanisms of disease resistance in pear.
Collapse
Affiliation(s)
- Manyi Sun
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Mingyue Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jugpreet Singh
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | - Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zikai Tang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yueyuan Liu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Runze Wang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Mengfan Qin
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Awais Khan
- Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA.
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| |
Collapse
|
8
|
Mapping Gene Markers for Apple Fruit Ring Rot Disease Resistance Using a Multi-omics Approach. G3-GENES GENOMES GENETICS 2019; 9:1663-1678. [PMID: 30910819 PMCID: PMC6505150 DOI: 10.1534/g3.119.400167] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Apple fruit ring rot (FRR), caused by Botryosphaeria dothidea, is a worldwide disease that impacts Asian apple production regions. However, no substantial progress has thus far been made toward the mapping of candidate genes or the development of effective genetic makers. In this five-year study, the resistance of 1,733 F1 hybrids from the cross ‘Jonathan’ × ‘Golden Delicious’ was phenotyped by non-wounding inoculation with four B. dothidea isolates. We first conducted systematic comparison of different analytic strategies for bulk segregant analysis by re-sequencing (BSA-Seq) and obtained suitable one for outbreeding species such as Malus. Forty-six quantitative trait loci (QTL) for resistance/susceptibility to the four isolates, including one QTL ‘hotspot’ on chromosome 14, were identified via BSA-Seq. Using integrated multi-omics strategies including RNA-sequencing, parental re-sequencing, BSA-Seq and meta-analysis of RNA-sequencing, fifty-seven candidate genes and corresponding functional mutations from the QTL were predicted. Functional mutations located on the candidate genes were validated using kompetitive allele-specific PCR in hybrids and Malus germplasm accessions with extremely resistant/susceptible phenotypes. Ten effective markers for apple ring rot were developed. The results provide an example of rapid candidate gene mapping for complex traits in outbreeding species.
Collapse
|
9
|
Moriya S, Terakami S, Okada K, Shimizu T, Adachi Y, Katayose Y, Fujisawa H, Wu J, Kanamori H, Yamamoto T, Abe K. Identification of candidate genes responsible for the susceptibility of apple (Malus × domestica Borkh.) to Alternaria blotch. BMC PLANT BIOLOGY 2019; 19:132. [PMID: 30961541 PMCID: PMC6454750 DOI: 10.1186/s12870-019-1737-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/24/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The mechanism underlying the interaction between host plant and host-selective toxin (HST)-producing Alternaria alternata during infection is of particular interest for sustainable crop production. Alternaria blotch of apple (Malus × domestica Borkh.) caused by A. alternata apple pathotype is a major disease particularly in East Asia, which is the largest producer of apples globally. A single dominant gene, Alt, controls the susceptibility of the apple cultivar 'Delicious' to Alternaria blotch. In this study, we fine mapped the Alt locus and characterized three potential candidate genes. RESULTS We used 797 F1 individuals derived from 15 crosses between apple accessions susceptible (Alt/alt) and resistant (alt/alt) to Alternaria blotch to construct physical and genetic maps of the Alt locus located on the top of chromosome 11. Susceptible accessions were derived from 'Delicious.' To fine map the Alt locus, we constructed a BAC library of 'Starking Delicious,' a sport of 'Delicious,' and used graphical genotyping to delimit the Alt locus to a region of 43 kb. Three genes predicted within the candidate Alt region were potentially involved in plant defense response, among which the gene encoding a coiled coil-nucleotide binding-leucine rich repeat (CC-NB-LRR) type disease resistance protein was the most promising. Moreover, a 12-bp insertion was uniquely identified in the 5' untranslated region of the Alt-associated allele of this gene, the presence or absence of which co-segregated with the susceptibility or resistance to A. alternata apple pathotype, respectively, among 43 tested cultivars including old ones and founders of modern apple breeding. CONCLUSION A disease resistance protein has been suggested as a determinant of susceptibility/resistance to HST-producing A. alternata for the first time. Our finding provides new insight into the mechanism of HST-mediated disease control used by A. alternata against host plants.
Collapse
Affiliation(s)
- Shigeki Moriya
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123 Japan
| | - Shingo Terakami
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8604 Japan
| | - Kazuma Okada
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123 Japan
| | - Taku Shimizu
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123 Japan
| | - Yoshihiko Adachi
- Citrus Research Station, Institute of Fruit Tree and Tea Science, NARO, 485-6 Okitsunaka-cho, Shimizu, Shizuoka City, Shizuoka 424-0284 Japan
| | - Yuichi Katayose
- Advanced Genomics Breeding Section, Institute of Crop Science, NARO, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634 Japan
| | - Hiroko Fujisawa
- Advanced Genomics Breeding Section, Institute of Crop Science, NARO, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634 Japan
| | - Jianzhon Wu
- Advanced Genomics Breeding Section, Institute of Crop Science, NARO, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634 Japan
| | - Hiroyuki Kanamori
- Advanced Genomics Breeding Section, Institute of Crop Science, NARO, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634 Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8604 Japan
| | - Kazuyuki Abe
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate 020-0123 Japan
| |
Collapse
|
10
|
Jeger M, Bragard C, Caffier D, Candresse T, Chatzivassiliou E, Dehnen-Schmutz K, Gilioli G, Grégoire JC, Jaques Miret JA, MacLeod A, Navajas Navarro M, Niere B, Parnell S, Potting R, Rafoss T, Urek G, Van Bruggen A, Van der Werf W, West J, Winter S, Vicent A, Vloutoglou I, Bottex B, Rossi V. Pest categorisation of small-spored Alternaria carrying the genes for the AM- or AK-toxin biosynthesis. EFSA J 2017; 15:e05099. [PMID: 32625384 PMCID: PMC7009986 DOI: 10.2903/j.efsa.2017.5099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Panel on Plant Health performed a pest categorisation of small‐spored Alternaria carrying the genes for the AM‐ or AK‐toxin biosynthesis, for the EU. The identity of the pests is clearly defined and reliable methods exist for their detection/identification. They are listed in Annex IIAI of Directive 2000/29/EC as Alternaria alternata (non‐European pathogenic isolates). Their distribution in the EU is restricted though with some uncertainty. The AM‐toxin producer Alternaria affect Malus spp. and Pyrus communis (European pear), whereas the AK‐toxin producer affect Pyrus pyrifolia, Pyrus bretschneideri and Pyrus ussuriensis (Asian pears). The pests could potentially enter the EU on host‐planting material and fruit originating in infested countries. There are no biotic/abiotic factors limiting their potential establishment and spread in the EU, as their epidemiology is similar to that of other well‐established Alternaria spp. Apples and European pears are widespread in the EU; Japanese pears are also present, but no data was found on their abundance/distribution. In the infested areas, the pests cause premature defoliation, fruit spotting and rot resulting in yield/quality losses. It is expected that the introduction and spread of the pests in the EU could impact apple and pear production, although the magnitude is unknown. Cultural practices and chemical measures may reduce the inoculum and the disease, but they cannot eliminate the pests. Phytosanitary measures are available to mitigate the risk of introduction and spread of the pests. The pests do not meet all the criteria assessed by EFSA for consideration as potential Union quarantine pests, as they are not under official control in those EU restricted areas where they have been found. The pests do not meet all the criteria assessed by EFSA to consider them as Union regulated non‐quarantine pests, as host plants for planting are not the main means of pest spread.
Collapse
|
11
|
Li L, Deng CH, Knäbel M, Chagné D, Kumar S, Sun J, Zhang S, Wu J. Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome. DNA Res 2017; 24:289-301. [PMID: 28130382 PMCID: PMC5499846 DOI: 10.1093/dnares/dsw063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 12/16/2016] [Indexed: 01/14/2023] Open
Abstract
Genetic maps are essential tools for pear genetics and genomics research. In this study, we first constructed an integrated simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)-based consensus genetic map for pear based on common SSR markers between nine published maps. A total of 5,085 markers, including 1,232 SSRs and 3,853 SNPs, were localized on a consensus map spanning 3,266.0 cM in total, with an average marker interval of 0.64 cM, which represents the highest density consensus map of pear to date. Using three sets of high-density SNP-based genetic maps with European pear genetic backgrounds, we anchored a total of 291.5 Mb of the ‘Bartlett’ v1.0 (Pyrus communis L.) genome scaffolds into 17 pseudo-chromosomes. This accounted for 50.5% of the genome assembly, which was a great improvement on the 29.7% achieved originally. Intra-genome and inter-genome synteny analyses of the new ‘Bartlett’ v1.1 genome assembly with the Asian pear ‘Dangshansuli’ (Pyrus bretschneideri Rehd.) and apple (Malus × domestica Borkh.) genomes uncovered four new segmental duplication regions. The integrated high-density SSR and SNP-based consensus genetic map provided new insights into the genetic structure patterns of pear and assisted in the genome assembly of ‘Bartlett’ through further exploration of different pear genetic maps.
Collapse
Affiliation(s)
- Leiting Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand
| | - Mareike Knäbel
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand
| | - David Chagné
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand
| | - Satish Kumar
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand
| | - Jiangmei Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| | - Jun Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
12
|
de Azevedo Peixoto L, Laviola BG, Alves AA, Rosado TB, Bhering LL. Breeding Jatropha curcas by genomic selection: A pilot assessment of the accuracy of predictive models. PLoS One 2017; 12:e0173368. [PMID: 28296913 PMCID: PMC5351973 DOI: 10.1371/journal.pone.0173368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/20/2017] [Indexed: 11/19/2022] Open
Abstract
Genomic wide selection is a promising approach for improving the selection accuracy in plant breeding, particularly in species with long life cycles, such as Jatropha. Therefore, the objectives of this study were to estimate the genetic parameters for grain yield (GY) and the weight of 100 seeds (W100S) using restricted maximum likelihood (REML); to compare the performance of GWS methods to predict GY and W100S; and to estimate how many markers are needed to train the GWS model to obtain the maximum accuracy. Eight GWS models were compared in terms of predictive ability. The impact that the marker density had on the predictive ability was investigated using a varying number of markers, from 2 to 1,248. Because the genetic variance between evaluated genotypes was significant, it was possible to obtain selection gain. All of the GWS methods tested in this study can be used to predict GY and W100S in Jatropha. A training model fitted using 1,000 and 800 markers is sufficient to capture the maximum genetic variance and, consequently, maximum prediction ability of GY and W100S, respectively. This study demonstrated the applicability of genome-wide prediction to identify useful genetic sources of GY and W100S for Jatropha breeding. Further research is needed to confirm the applicability of the proposed approach to other complex traits.
Collapse
Affiliation(s)
| | - Bruno Galvêas Laviola
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Agroenergia, Parque Estação Biológica–PqEB s/n, Asa Norte, Brasília, Brazil
| | - Alexandre Alonso Alves
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Agroenergia, Parque Estação Biológica–PqEB s/n, Asa Norte, Brasília, Brazil
| | - Tatiana Barbosa Rosado
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Agroenergia, Parque Estação Biológica–PqEB s/n, Asa Norte, Brasília, Brazil
| | | |
Collapse
|
13
|
Yamamoto M, Terakami S, Takada N, Yamamoto T. Physical mapping of black spot disease resistance/susceptibility-related genome regions in Japanese pear (Pyrus pyrifolia) by BAC-FISH. BREEDING SCIENCE 2016; 66:444-9. [PMID: 27436955 PMCID: PMC4902454 DOI: 10.1270/jsbbs.15085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/19/2016] [Indexed: 06/06/2023]
Abstract
Black spot disease, caused by Alternaria alternata Japanese pear pathotype, is one of the most harmful diseases in Japanese pear cultivation. In the present study, the locations of black spot disease resistance/susceptibility-related genome regions were studied by fluorescence in situ hybridization using BAC clone (BAC-FISH) on Japanese pear (Pyrus pyrifolia (Burm. f.) Nakai) chromosomes. Root tips of self-pollinated seedlings of 'Osa Gold' were used as materials. Chromosome samples were prepared by the enzymatic maceration and air-drying method. The BAC clone adjacent to the black spot disease-related gene was labeled as a probe for FISH analysis. Black spot disease-related genome regions were detected in telomeric positions of two medium size chromosomes. These two sites and six telomeric 18S-5.8S-25S rDNA sites were located on different chromosomes as determined from the results of multi-color FISH. The effectiveness of the physical mapping of useful genes on pear chromosomes achieved by the BAC-FISH method was unequivocally demonstrated.
Collapse
Affiliation(s)
- Masashi Yamamoto
- Faculty of Agriculture, Kagoshima University,
Korimoto, Kagoshima 890-0065,
Japan
| | - Shingo Terakami
- NARO Institute of Fruit Tree Science,
Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Norio Takada
- NARO Institute of Fruit Tree Science,
Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Toshiya Yamamoto
- NARO Institute of Fruit Tree Science,
Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| |
Collapse
|