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Sandhu N, Singh J, Ankush AP, Augustine G, Raigar OP, Verma VK, Pruthi G, Kumar A. Development of Novel KASP Markers for Improved Germination in Deep-Sown Direct Seeded Rice. RICE (NEW YORK, N.Y.) 2024; 17:33. [PMID: 38727876 PMCID: PMC11087395 DOI: 10.1186/s12284-024-00711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND The lack of stable-high yielding and direct-seeded adapted varieties with better germination ability from deeper soil depth and availability of molecular markers are major limitation in achieving the maximum yield potential of rice under water and resource limited conditions. Development of high-throughput and trait-linked markers are of great interest in genomics-assisted breeding. The aim of present study was to develop and validate novel KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving germination and seedling vigor of deep sown direct seeded rice (DSR). RESULTS Out of 58 designed KASP assays, four KASP assays did not show any polymorphism in any of the eleven genetic backgrounds considered in the present study. The 54 polymorphic KASP assays were then validated for their robustness and reliability on the F1s plants developed from eight different crosses considered in the present study. The third next validation was carried out on 256 F3:F4 and 713 BC3F2:3 progenies. Finally, the reliability of the KASP assays was accessed on a set of random 50 samples from F3:F4 and 80-100 samples from BC3F2:3 progenies using the 10 random markers. From the 54 polymorphic KASP, based on the false positive rate, false negative rate, KASP utility in different genetic backgrounds and significant differences in the phenotypic values of the positive (desirable) and negative (undesirable) traits, a total of 12 KASP assays have been selected. These 12 KASP include 5 KASP on chromosome 3, 1 on chromosome 4, 3 on chromosome 7 and 3 on chromosome 8. The two SNPs lying in the exon regions of LOC_Os04g34290 and LOC_Os08g32100 led to non-synonymous mutations indicating a possible deleterious effect of the SNP variants on the protein structure. CONCLUSION The present research work will provide trait-linked KASP assays, improved breeding material possessing favourable alleles and breeding material in form of expected pre-direct-seeded adapted rice varieties. The marker can be utilized in introgression program during pyramiding of valuable QTLs/genes providing adaptation to rice under DSR. The functional studies of the genes LOC_Os04g34290 and LOC_Os08g32100 possessing two validated SNPs may provide valuable information about these genes.
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Affiliation(s)
- Nitika Sandhu
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Jasneet Singh
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | | | | | | | - Gomsie Pruthi
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Arvind Kumar
- Delta Agrigenetics, Plot No. 99 & 100 Green Park Avenue, Village, Jeedimetla, Secunderabad, Telangana, 500055, India
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Xing X, Hu T, Wang Y, Li Y, Wang W, Hu H, Wei Q, Yan Y, Gan D, Bao C, Wang J. Construction of SNP fingerprints and genetic diversity analysis of radish ( Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1329890. [PMID: 38371408 PMCID: PMC10869463 DOI: 10.3389/fpls.2024.1329890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/20/2024]
Abstract
Radish (Raphanus sativus L.) is a vegetable crop with economic value and ecological significance in the genus Radish, family Brassicaceae. In recent years, developed countries have attached great importance to the collection and conservation of radish germplasm resources and their research and utilization, but the lack of population genetic information and molecular markers has hindered the development of the genetic breeding of radish. In this study, we integrated the radish genomic data published in databases for the development of single-nucleotide polymorphism (SNP) markers, and obtained a dataset of 308 high-quality SNPs under strict selection criteria. With the support of Kompetitive Allele-Specific PCR (KASP) technology, we screened a set of 32 candidate core SNP marker sets to analyse the genetic diversity of the collected 356 radish varieties. The results showed that the mean values of polymorphism information content (PIC), minor allele frequency (MAF), gene diversity and heterozygosity of the 32 candidate core SNP markers were 0.32, 0.30, 0.40 and 0.25, respectively. Population structural analysis, principal component analysis and genetic evolutionary tree analysis indicated that the 356 radish materials were best classified into two taxa, and that the two taxa of the material were closely genetically exchanged. Finally, on the basis of 32 candidate core SNP markers we calculated 15 core markers using a computer algorithm to construct a fingerprint map of 356 radish varieties. Furthermore, we constructed a core germplasm population consisting of 71 radish materials using 32 candidate core markers. In this study, we developed SNP markers for radish cultivar identification and genetic diversity analysis, and constructed DNA fingerprints, providing a basis for the identification of radish germplasm resources and molecular marker-assisted breeding as well as genetic research.
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Affiliation(s)
- Xiaolin Xing
- School of Horticulture, Anhui Agricultural University, Hefei, China
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Tianhua Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yikui Wang
- Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yan Li
- Institute of Vegetables, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wuhong Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haijiao Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qingzhen Wei
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaqin Yan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Defang Gan
- School of Horticulture, Anhui Agricultural University, Hefei, China
| | - Chonglai Bao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jinglei Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Yang Q, Zhang J, Shi X, Chen L, Qin J, Zhang M, Yang C, Song Q, Yan L. Development of SNP marker panels for genotyping by target sequencing (GBTS) and its application in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:26. [PMID: 37313526 PMCID: PMC10248699 DOI: 10.1007/s11032-023-01372-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/16/2023] [Indexed: 06/15/2023]
Abstract
A high-throughput genotyping platform with customized flexibility, high genotyping accuracy, and low cost is critical for marker-assisted selection and genetic mapping in soybean. Three assay panels were selected from the SoySNP50K, 40K, 20K, and 10K arrays, containing 41,541, 20,748, and 9670 SNP markers, respectively, for genotyping by target sequencing (GBTS). Fifteen representative accessions were used to assess the accuracy and consistency of the SNP alleles identified by the SNP panels and sequencing platform. The SNP alleles were 99.87% identical between technical replicates and 98.86% identical between the 40K SNP GBTS panel and 10× resequencing analysis. The GBTS method was also accurate in the sense that the genotypic dataset of the 15 representative accessions correctly revealed the pedigree of the accessions, and the biparental progeny datasets correctly constructed the linkage maps of the SNPs. The 10K panel was also used to genotype two parent-derived populations and analyze QTLs controlling 100-seed weight, resulting in the identification of the stable associated genetic locus Locus_OSW_06 on chromosome 06. The markers flanking the QTL explained 7.05% and 9.83% of the phenotypic variation, respectively. Compared with GBS and DNA chips, the 40K, 20K, and 10K panels reduced costs by 5.07% and 58.28%, 21.44% and 65.48%, and 35.74% and 71.76%, respectively. Low-cost genotyping panels could facilitate soybean germplasm assessment, genetic linkage map construction, QTL identification, and genomic selection. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01372-6.
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Affiliation(s)
- Qing Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Jianan Zhang
- Mol Breeding Biotechnology Co., Ltd., 136 Huanghe Parkway, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Lei Chen
- School of Life Sciences, Yantai University, 30# Qingquan Road, Lai Shan District, Yantai, 264005 Shandong People’s Republic of China
| | - Jun Qin
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD USA
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
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Ishwarya Lakshmi VG, Sreedhar M, JhansiLakshmi V, Gireesh C, Rathod S, Bohar R, Deshpande S, Laavanya R, Kiranmayee KNSU, Siddi S, Vanisri S. Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice. Front Genet 2022; 13:914131. [PMID: 35899197 PMCID: PMC9309266 DOI: 10.3389/fgene.2022.914131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Rice (Oryza sativa L.) is an important source of nutrition for the world’s burgeoning population that often faces yield loss due to infestation by the brown planthopper (BPH, Nilaparvata lugens (Stål)). The development of rice cultivars with BPH resistance is one of the crucial precedences in rice breeding programs. Recent progress in high-throughput SNP-based genotyping technology has made it possible to develop markers linked to the BPH more quickly than ever before. With this view, a genome-wide association study was undertaken for deriving marker-trait associations with BPH damage scores and SNPs from genotyping-by-sequencing data of 391 multi-parent advanced generation inter-cross (MAGIC) lines. A total of 23 significant SNPs involved in stress resistance pathways were selected from a general linear model along with 31 SNPs reported from a FarmCPU model in previous studies. Of these 54 SNPs, 20 were selected in such a way to cover 13 stress-related genes. Kompetitive allele-specific PCR (KASP) assays were designed for the 20 selected SNPs and were subsequently used in validating the genotypes that were identified, six SNPs, viz, snpOS00912, snpOS00915, snpOS00922, snpOS00923, snpOS00927, and snpOS00929 as efficient in distinguishing the genotypes into BPH-resistant and susceptible clusters. Bph17 and Bph32 genes that are highly effective against the biotype 4 of the BPH have been validated by gene specific SNPs with favorable alleles in M201, M272, M344, RathuHeenati, and RathuHeenati accession. These identified genotypes could be useful as donors for transferring BPH resistance into popular varieties with marker-assisted selection using these diagnostic SNPs. The resistant lines and the significant SNPs unearthed from our study can be useful in developing BPH-resistant varieties after validating them in biparental populations with the potential usefulness of SNPs as causal markers.
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Affiliation(s)
- V. G. Ishwarya Lakshmi
- Department of Genetics and Plant Breeding, College of Agriculture, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - M. Sreedhar
- Administrative Office, PJTSAU, Hyderabad, India
| | | | - C. Gireesh
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Santosha Rathod
- ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Rajaguru Bohar
- CGIAR Excellence in Breeding (EiB), CIMMYT-ICRISAT, Hyderabad, India
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - R. Laavanya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | | | - Sreedhar Siddi
- Agricultural Research Station, PJTSAU, Peddapalli, India
| | - S. Vanisri
- Institute of Biotechnology, PJTSAU, Hyderabad, India
- *Correspondence: S. Vanisri,
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Guo Y, Li B, Li M, Zhu H, Yang Q, Liu X, Qu L, Fan L, Wang T. Efficient marker-assisted breeding for clubroot resistance in elite Pol-CMS rapeseed varieties by updating the PbBa8.1 locus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:41. [PMID: 37313506 PMCID: PMC10248692 DOI: 10.1007/s11032-022-01305-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Clubroot disease poses a severe threat to rapeseed (Brassica napus) production worldwide and has recently been spreading across China at an unprecedented pace. Breeding and cultivation of resistant varieties constitute a promising and environment-friendly approach to mitigating this threat. In this study, the clubroot resistance locus PbBa8.1 was successfully transferred into SC4, a shared paternal line of three elite varieties in five generations by marker-assisted backcross breeding. Kompetitive allele specific PCR (KASP) markers of clubroot resistance gene PbBa8.1 and its linked high erucic acid gene (FAE1) were designed and applied for foreground selection, and 1,000 single-nucleotide polymorphisms (SNPs) were selected and used for the background selection. This breeding strategy produced recombinants with the highest recovery ratio of the recurrent parent genome (> 95%) at BC2F2 while breaking the linkage with FAE1 during the selection. An updated version of the paternal line (SC4R) was generated at BC2F3, showing significantly improved clubroot resistance at the seedling stage via artificial inoculation, and was comparable to that of the donor parent. Field trials of the three elite varieties and their updated versions in five environments indicated similar agronomic appearance and final yield. The introduced breeding strategy precisely pyramids the PbBa8.1 and FAE1 loci with the assistance of technical markers in a shorter period and could be applied to other desirable traits for directional improvement in the future. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01305-9.
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Affiliation(s)
- Yiming Guo
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Bao Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Mei Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Hongjian Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128 China
| | - Qian Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Xinhong Liu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Liang Qu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Lianyi Fan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
| | - Tonghua Wang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125 China
- Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Changsha, 410125 China
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Radanović A, Sprycha Y, Jocković M, Sundt M, Miladinović D, Jansen C, Horn R. KASP Markers Specific for the Fertility Restorer Locus Rf1 and Application for Genetic Purity Testing in Sunflowers (Helianthus annuus L.). Genes (Basel) 2022; 13:genes13030465. [PMID: 35328019 PMCID: PMC8951052 DOI: 10.3390/genes13030465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) were significantly associated with fertility restoration of cytoplasmic male sterility (CMS) PET1 by the restorer gene Rf1. For these SNPs, four Kompetitive allele-specific PCR (KASP) markers were successfully designed. The KASP markers cover the fertility restorer locus Rf1, spanning about 3 Mb, and clearly differentiate restorer and maintainer lines. For genetic purity testing in sunflower hybrid production, the efficiency for detecting contaminations in samples was simulated using mixtures of hypocotyls or leaves. Contaminations of restorer lines with 1%, 3%, 5%, 10%, and 50% of maintainer lines were screened with all four KASP markers. Contaminations of 10% could be clearly detected in pools of 100 plants. Contaminations below this level require detection on a single plant level. For single plant detections, ethyl methanesulfonate-treated sunflower F1 hybrids, which had been phenotypically evaluated for male sterility (potential mutation in the Rf1 gene) were screened. Nine identified either partially male-sterile or male-sterile plants were analyzed with all four KASP markers and only one proved to be a hybrid with a mutation, seven were male-sterile contaminants in the F1 seeds used (1.6%) and one a recombinant plant. The four KASP markers should be valuable tools for marker-assisted selection (MAS) in sunflower breeding regarding the restorer locus Rf1.
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Affiliation(s)
- Aleksandra Radanović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (A.R.); (M.J.); (D.M.)
| | - Yves Sprycha
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany; (Y.S.); (M.S.)
| | - Milan Jocković
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (A.R.); (M.J.); (D.M.)
| | - Monja Sundt
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany; (Y.S.); (M.S.)
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (A.R.); (M.J.); (D.M.)
| | - Constantin Jansen
- Strube Research GmbH & Co. KG, Hauptstr. 1, D-38387 Söllingen, Germany;
| | - Renate Horn
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany; (Y.S.); (M.S.)
- Correspondence:
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Gao Y, Zhou S, Huang Y, Zhang B, Xu Y, Zhang G, Lakshmanan P, Yang R, Zhou H, Huang D, Liu J, Tan H, He W, Yang C, Duan W. Quantitative Trait Loci Mapping and Development of KASP Marker Smut Screening Assay Using High-Density Genetic Map and Bulked Segregant RNA Sequencing in Sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2022; 12:796189. [PMID: 35069651 PMCID: PMC8766830 DOI: 10.3389/fpls.2021.796189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/13/2021] [Indexed: 06/02/2023]
Abstract
Sugarcane is one of the most important industrial crops globally. It is the second largest source of bioethanol, and a major crop for biomass-derived electricity and sugar worldwide. Smut, caused by Sporisorium scitamineum, is a major sugarcane disease in many countries, and is managed by smut-resistant varieties. In China, smut remains the single largest constraint for sugarcane production, and consequently it impacts the value of sugarcane as an energy feedstock. Quantitative trait loci (QTLs) associated with smut resistance and linked diagnostic markers are valuable tools for smut resistance breeding. Here, we developed an F1 population (192 progeny) by crossing two sugarcane varieties with contrasting smut resistance and used for genome-wide single nucleotide polymorphism (SNP) discovery and mapping, using a high-throughput genotyping method called "specific locus amplified fragment sequencing (SLAF-seq) and bulked-segregant RNA sequencing (BSR-seq). SLAF-seq generated 148,500 polymorphic SNP markers. Using SNP and previously identified SSR markers, an integrated genetic map with an average 1.96 cM marker interval was produced. With this genetic map and smut resistance scores of the F1 individuals from four crop years, 21 major QTLs were mapped, with a phenotypic variance explanation (PVE) > 8.0%. Among them, 10 QTLs were stable (repeatable) with PVEs ranging from 8.0 to 81.7%. Further, four QTLs were detected based on BSR-seq analysis. aligning major QTLs with the genome of a sugarcane progenitor Saccharum spontaneum, six markers were found co-localized. Markers located in QTLs and functional annotation of BSR-seq-derived unigenes helped identify four disease resistance candidate genes located in major QTLs. 77 SNPs from major QTLs were then converted to Kompetitive Allele-Specific PCR (KASP) markers, of which five were highly significantly linked to smut resistance. The co-localized QTLs, candidate resistance genes, and KASP markers identified in this study provide practically useful tools for marker-assisted sugarcane smut resistance breeding.
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Affiliation(s)
- Yijing Gao
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Shan Zhou
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Yuxin Huang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Baoqing Zhang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, China
| | - Gemin Zhang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Prakash Lakshmanan
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing, China
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, Australia
| | - Rongzhong Yang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Hui Zhou
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Dongliang Huang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Junxian Liu
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Hongwei Tan
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weizhong He
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Cuifang Yang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Weixing Duan
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Sugarcane Research Center, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Nanning, China
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Genome-wide association analysis of chickpea germplasms differing for salinity tolerance based on DArTseq markers. PLoS One 2021; 16:e0260709. [PMID: 34852014 PMCID: PMC8635330 DOI: 10.1371/journal.pone.0260709] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
Soil salinity is significant abiotic stress that severely limits global crop production. Chickpea (Cicer arietinum L.) is an important grain legume that plays a substantial role in nutritional food security, especially in the developing world. This study used a chickpea population collected from the International Center for Agricultural Research in the Dry Area (ICARDA) genebank using the focused identification of germplasm strategy. The germplasm included 186 genotypes with broad Asian and African origins and genotyped with 1856 DArTseq markers. We conducted phenotyping for salinity in the field (Arish, Sinai, Egypt) and greenhouse hydroponic experiments at 100 mM NaCl concentration. Based on the performance in both hydroponic and field experiments, we identified seven genotypes from Azerbaijan and Pakistan (IGs: 70782, 70430, 70764, 117703, 6057, 8447, and 70249) as potential sources for high salinity tolerance. Multi-trait genome-wide association analysis (mtGWAS) detected one locus on chromosome Ca4 at 10618070 bp associated with salinity tolerance under hydroponic and field conditions. In addition, we located another locus specific to the hydroponic system on chromosome Ca2 at 30537619 bp. Gene annotation analysis revealed the location of rs5825813 within the Embryogenesis-associated protein (EMB8-like), while the location of rs5825939 is within the Ribosomal Protein Large P0 (RPLP0). Utilizing such markers in practical breeding programs can effectively improve the adaptability of current chickpea cultivars in saline soil. Moreover, researchers can use our markers to facilitate the incorporation of new genes into commercial cultivars.
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Gill KS, Kaur G, Kaur G, Kaur J, Kaur Sra S, Kaur K, Gurpreet K, Sharma M, Bansal M, Chhuneja P, Banga SS. Development and Validation of Kompetitive Allele-Specific PCR Assays for Erucic Acid Content in Indian Mustard [ Brassica juncea (L.) Czern and Coss.]. FRONTIERS IN PLANT SCIENCE 2021; 12:738805. [PMID: 34975937 PMCID: PMC8714676 DOI: 10.3389/fpls.2021.738805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/20/2021] [Indexed: 05/10/2023]
Abstract
Brassica juncea L. is the most widely cultivated oilseed crop in Indian subcontinent. Its seeds contain oil with very high concentration of erucic acid (≈50%). Of late, there is increasing emphasis on the development of low erucic acid varieties because of reported association of the consumption of high erucic acid oil with cardiac lipidosis. Erucic acid is synthesized from oleic acid by an elongation process involving two cycles of four sequential steps. Of which, the first step is catalyzed by β-ketoacyl-CoA synthase (KCS) encoded by the fatty acid elongase 1 (FAE1) gene in Brassica. Mutations in the coding region of the FAE1 lead to the loss of KCS activity and consequently a drastic reduction of erucic acid in the seeds. Molecular markers have been developed on the basis of variation available in the coding or promoter region(s) of the FAE1. However, majority of these markers are not breeder friendly and are rarely used in the breeding programs. Present studies were planned to develop robust kompetitive allele-specific PCR (KASPar) assays with high throughput and economics of scale. We first cloned and sequenced FAE1.1 and FAE1.2 from high and low erucic acid (<2%) genotypes of B. juncea (AABB) and its progenitor species, B. rapa (AA) and B. nigra (BB). Sequence comparisons of FAE1.1 and FAE1.2 genes for low and high erucic acid genotypes revealed single nucleotide polymorphisms (SNPs) at 8 and 3 positions. Of these, three SNPs for FAE1.1 and one SNPs for FAE1.2 produced missense mutations, leading to amino acid modifications and inactivation of KCS enzyme. We used SNPs at positions 735 and 1,476 for genes FAE1.1 and FAE1.2, respectively, to develop KASPar assays. These markers were validated on a collection of diverse genotypes and a segregating backcross progeny. KASPar assays developed in this study will be useful for marker-assisted breeding, as these can track recessive alleles in their heterozygous state with high reproducibility.
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Affiliation(s)
- Karanjot Singh Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Gurpreet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Gurpreet Kaur, ; orcid.org/0000-0002-0660-9592
| | - Gurdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Jasmeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Simarjeet Kaur Sra
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Kawalpreet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Kaur Gurpreet
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Meha Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Mitaly Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Surinder S. Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
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