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Dallinger HG, Löschenberger F, Azrak N, Ametz C, Michel S, Bürstmayr H. Genome-wide association mapping for pre-harvest sprouting in European winter wheat detects novel resistance QTL, pleiotropic effects, and structural variation in multiple genomes. THE PLANT GENOME 2024; 17:e20301. [PMID: 36851839 DOI: 10.1002/tpg2.20301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/20/2022] [Indexed: 06/18/2023]
Abstract
Pre-harvest sprouting (PHS), germination of seeds before harvest, is a major problem in global wheat (Triticum aestivum L.) production, and leads to reduced bread-making quality in affected grain. Breeding for PHS resistance can prevent losses under adverse conditions. Selecting resistant lines in years lacking pre-harvest rain, requires challenging of plants in the field or in the laboratory or using genetic markers. Despite the availability of a wheat reference and pan-genome, linking markers, genes, allelic, and structural variation, a complete understanding of the mechanisms underlying various sources of PHS resistance is still lacking. Therefore, we challenged a population of European wheat varieties and breeding lines with PHS conditions and phenotyped them for PHS traits, grain quality, phenological and agronomic traits to conduct genome-wide association mapping. Furthermore, we compared these marker-trait associations to previously reported PHS loci and evaluated their usefulness for breeding. We found markers associated with PHS on all chromosomes, with strong evidence for novel quantitative trait locus/loci (QTL) on chromosome 1A and 5B. The QTL on chromosome 1A lacks pleiotropic effect, for the QTL on 5B we detected pleiotropic effects on phenology and grain quality. Multiple peaks on chromosome 4A co-located with the major resistance locus Phs-A1, for which two causal genes, TaPM19 and TaMKK3, have been proposed. Mapping markers and genes to the pan-genome and chromosomal alignments provide evidence for structural variation around this major PHS-resistance locus. Although PHS is controlled by many loci distributed across the wheat genome, Phs-A1 on chromosome 4A seems to be the most effective and widely deployed source of resistance, in European wheat varieties.
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Affiliation(s)
- Hermann G Dallinger
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, Tulln, Austria
- Saatzucht Donau GesmbH & Co KG, Saatzuchtstrasse 11, Probstdorf, Austria
| | | | - Naim Azrak
- Saatzucht Donau GesmbH & Co KG, Saatzuchtstrasse 11, Probstdorf, Austria
| | - Christian Ametz
- Saatzucht Donau GesmbH & Co KG, Saatzuchtstrasse 11, Probstdorf, Austria
| | - Sebastian Michel
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, Tulln, Austria
| | - Hermann Bürstmayr
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, Tulln, Austria
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McGinty EM, Craine EB, Miller ND, Ocana-Gallegos C, Spalding EP, Murphy KM, Hauvermale AL. Evaluating relationships between seed morphological traits and seed dormancy in Chenopodium quinoa Willd. FRONTIERS IN PLANT SCIENCE 2023; 14:1161165. [PMID: 37929178 PMCID: PMC10623317 DOI: 10.3389/fpls.2023.1161165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Introduction Quinoa is a high-value, nutritious crop that performs well in variable environments, marginal soils, and in diverse crop rotations. Quinoa's many attributes make it an ideal crop for supporting human health in global communities and economies. To date, quinoa research has largely focused on traits in adult plants important for enhancing plant phenotypic plasticity, abiotic stress, disease resistance, and yield. Fewer studies have evaluated quinoa seed dormancy and suggest that most modern quinoa varieties have weak or no seed dormancy, and a narrow window of seed viability post-harvest. In other crops, diminished seed dormancy is a major risk factor for preharvest sprouting (PHS; germination on the panicle due to rain prior to harvest) and may also pose a similar risk for quinoa. Methods This study (1) developed a dormancy screening assay to characterize seed dormancy strength in a large collection of quinoa varieties, (2) investigated if morphological variables including seed coat color, seed coat thickness, seed shape including eccentricity which evaluates the roundness or flatness of a seed, and other agronomic traits like crude protein content and seed moisture, contribute to quinoa seed dormancy, and (3) evaluated the use of a phenetic modeling approach to explore relationships between seed morphology and seed dormancy. Results Dormancy screening indicated seed dormancy ranges in quinoa varieties from none to strong dormancy. Further, phenetic modeling approaches indicate that seed coat thickness and eccentricity are important morphological variables that impact quinoa seed dormancy strength. Conclusions While dormancy screening and phenetic modeling approaches do not provide a direct solution to preventing PHS in quinoa, they do provide new tools for identifying dormant varieties as well as morphological variables contributing to seed dormancy.
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Affiliation(s)
- Emma M. McGinty
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | | | - Nathan D. Miller
- Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Cristina Ocana-Gallegos
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin, Madison, WI, United States
| | - Kevin M. Murphy
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Amber L. Hauvermale
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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Haile M, Ro N, Ko HC, Oh H, Lee GA. A Comprehensive Genome-Wide Association Study of Carotenoid and Capsaicinoid Contents in Capsicum chinense Germplasm. Int J Mol Sci 2023; 24:13885. [PMID: 37762188 PMCID: PMC10531199 DOI: 10.3390/ijms241813885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Pepper is a highly important vegetable globally, both economically and nutritionally. However, to efficiently select and identify genetic resources for pepper breeding programs, it is crucial to understand the association between important traits and genetic factors. In this study, we investigated the genetic basis of carotenoid and capsaicinoid content in 160 Capsicum chinense germplasms. The study observed significant variability in carotenoid and capsaicinoid content among the germplasms. Correlation analysis revealed a strong positive correlation between violaxanthin and antheraxanthin. In contrast, capsaicin and dihydrocapsaicin displayed negative correlations with individual carotenoids but exhibited a strong positive correlation between the two compounds (r = 0.90 ***). Genotyping-by-sequencing (GBS) was performed on 160 genotypes of pepper germplasm, which identified 47,810 high-quality SNPs. A comprehensive genome-wide association analysis was performed using these SNPs to identify SNPs associated with carotenoids and capsaicinoids, revealing 193 SNPs that exhibited significant associations. Specifically, 4 SNPs were associated with violaxanthin, 2 with antheraxanthin, 86 with capsorubin, 5 with capsanthin, 63 with zeaxanthin, 3 with β-cryptoxanthin, and 2 with α-carotene. With further studies, the significantly associated SNPs identified in this study have the potential to be utilized for selecting pepper accessions with high carotenoid and capsaicinoid contents. Additionally, the genes associated with these significant SNPs will be used to understand their roles and involvement in the biosynthesis pathway of carotenoids and capsaicinoids. Understanding the function of these genes can provide insights into the molecular mechanisms underlying the production of these bioactive compounds in pepper. The findings of this study hold valuable implications for selecting pepper varieties with desirable traits and developing breeding programs aimed at enhancing the nutritional and medicinal properties of pepper.
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Pang Y, Liu C, Lin M, Ni F, Li W, Cai J, Zhang Z, Zhu H, Liu J, Wu J, Bai G, Liu S. Mapping QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Landrace. Int J Mol Sci 2022; 23:ijms23179662. [PMID: 36077059 PMCID: PMC9456275 DOI: 10.3390/ijms23179662] [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: 08/01/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Wheat stripe (yellow) rust is a worldwide disease that seriously reduces wheat grain yield and quality. Adult-plant resistance (APR) to stripe rust is generally more durable but usually controlled by multiple genes with partial resistance. In this study, a recombinant inbred line population was developed from a cross between a Chinese wheat landrace, Tutoumai, with APR to stripe rust, and a highly susceptible wheat cultivar, Siyang 936. The population was genotyped by genotyping-by-sequencing and phenotyped for APR to stripe rust in four consecutive field experiments. Three QTLs, QYr.sdau-1BL, QYr.sdau-5BL, and QYr.sdau-6BL, were identified for APR to stripe rust, and explained 8.0–21.2%, 10.1–22.7%, and 11.6–18.0% of the phenotypic variation, respectively. QYr.sdau-1BL was further mapped to a 21.6 Mb region using KASP markers derived from SNPs identified by RNA-seq of the two parents. In the QYr.sdau-1BL region, 13 disease-resistance-related genes were differently expressed between the two parents, and therefore were considered as the putative candidates of QYr.sdau-1BL. This study provides favorable gene/QTL and high-throughput markers to breeding programs for marker-assisted selection of the wheat stripe rust APR genes.
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Affiliation(s)
- Yunlong Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Chunxia Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Meng Lin
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Fei Ni
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Wenhui Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jin Cai
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Ziliang Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Huaqiang Zhu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jingxian Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
- Correspondence:
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Rabieyan E, Bihamta MR, Moghaddam ME, Mohammadi V, Alipour H. Genome-wide association mapping and genomic prediction for pre‑harvest sprouting resistance, low α-amylase and seed color in Iranian bread wheat. BMC PLANT BIOLOGY 2022; 22:300. [PMID: 35715737 PMCID: PMC9204952 DOI: 10.1186/s12870-022-03628-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Pre-harvest sprouting (PHS) refers to a phenomenon, in which the physiologically mature seeds are germinated on the spike before or during the harvesting practice owing to high humidity or prolonged period of rainfall. Pre-harvest sprouting (PHS) remarkably decreases seed quality and yield in wheat; hence it is imperative to uncover genomic regions responsible for PHS tolerance to be used in wheat breeding. A genome-wide association study (GWAS) was carried out using 298 bread wheat landraces and varieties from Iran to dissect the genomic regions of PHS tolerance in a well-irrigated environment. Three different approaches (RRBLUP, GBLUP and BRR) were followed to estimate prediction accuracies in wheat genomic selection. RESULTS Genomes B, A, and D harbored the largest number of significant marker pairs (MPs) in both landraces (427,017, 328,006, 92,702 MPs) and varieties (370,359, 266,708, 63,924 MPs), respectively. However, the LD levels were found the opposite, i.e., genomes D, A, and B have the highest LD, respectively. Association mapping by using GLM and MLM models resulted in 572 and 598 marker-trait associations (MTAs) for imputed SNPs (- log10 P > 3), respectively. Gene ontology exhibited that the pleitropic MPs located on 1A control seed color, α-Amy activity, and PHS. RRBLUP model indicated genetic effects better than GBLUP and BRR, offering a favorable tool for wheat genomic selection. CONCLUSIONS Gene ontology exhibited that the pleitropic MPs located on 1A can control seed color, α-Amy activity, and PHS. The verified markers in the current work can provide an opportunity to clone the underlying QTLs/genes, fine mapping, and genome-assisted selection.Our observations uncovered key MTAs related to seed color, α-Amy activity, and PHS that can be exploited in the genome-mediated development of novel varieties in wheat.
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Affiliation(s)
- Ehsan Rabieyan
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Mohammad Reza Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | | | - Valiollah Mohammadi
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
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Driskill M, Pardee K, Hummer KE, Zurn JD, Amundsen K, Wiles A, Wiedow C, Patzak J, Henning JA, Bassil NV. Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers. PLoS One 2022; 17:e0257746. [PMID: 35421090 PMCID: PMC9009645 DOI: 10.1371/journal.pone.0257746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/06/2022] [Indexed: 11/18/2022] Open
Abstract
Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set contains a sex-linked primer pair, HI-AGA7, that was used to genotype 629 hop accessions from the US Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR), the USDA Forage Seed and Cereal Research (FSCR), and the University of Nebraska-Lincoln (UNL) collections. The SSR set identified unique genotypes except for 89 sets of synonymous samples. These synonyms included: cultivars with different designations, the same cultivars from different sources, heat-treated clones, and clonal variants. Population structure analysis clustered accessions into wild North American (WNA) and cultivated groups. Diversity was slightly higher in the cultivated samples due to larger sample size. Parentage and sib-ship analyses were used to identify true-to-type cultivars. The HI-AGA7 marker generated two male- and nine female-specific alleles among the cultivated and WNA samples. The SSR and KASP fingerprinting sets were compared in 190 samples consisting of cultivated and WNA accession for their ability to confirm identity and assess diversity and population structure. The SSR fingerprinting set distinguished cultivars, selections and WNA accessions while the KASP assays were unable to distinguish the WNA samples and had lower diversity estimates than the SSR set. Both fingerprinting sets are valuable tools for identity confirmation and parentage analysis in hop for different purposes. The 9-SSR assay is cost efficient when genotyping a small number of wild and cultivated hop samples (<96) while the KASP assay is easy to interpret and cost efficient for genotyping a large number of cultivated samples (multiples of 96).
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Affiliation(s)
- Mandie Driskill
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Katie Pardee
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Kim E. Hummer
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Jason D. Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Keenan Amundsen
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Annette Wiles
- Midwest Hops Producers, Plattsmouth, Nebraska, United States of America
| | - Claudia Wiedow
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Josef Patzak
- Hop Research Institute, Co, Ltd., Žatec, Czech Republic
| | - John A. Henning
- USDA-ARS, Forage Seed and Cereal Research Unit, Corvallis, Oregon, United States of America
| | - Nahla V. Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
- * E-mail:
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Vuong TD, Sonah H, Patil G, Meinhardt C, Usovsky M, Kim KS, Belzile F, Li Z, Robbins R, Shannon JG, Nguyen HT. Identification of genomic loci conferring broad-spectrum resistance to multiple nematode species in exotic soybean accession PI 567305. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3379-3395. [PMID: 34297174 DOI: 10.1007/s00122-021-03903-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Genetic analysis identified a unique combination of major QTL for resistance to important soybean nematodes concurrently present in a single soybean accession, which has not been reported earlier. An exotic soybean [Glycine max (L.) Merr.] accession, PI 567305, was reported to be highly resistant to three important nematode species, soybean cyst (SCN), root-knot (RKN), and reniform (RN) nematodes. However, genetic basis controlling broad-spectrum resistance in this germplasm has not been investigated. We report results of genetic analysis to identify genomic loci conferring resistance to these nematode species. A bi-parental population consisting of 242 F8-derived recombinant inbred lines (RILs) was developed from a cross of a nematode susceptible cultivar, Magellan, and resistant accession, PI 567305. The RILs were phenotyped for nematode resistance to three SCN HG types. They were genotyped using the Infinium SoySNP6K BeadChips and genotype-by-sequencing (GBS) methods in an attempt to evaluate the cost-effectiveness and efficiency of these two genotyping platforms. Genetic analysis confirmed the major QTL on chromosomes (Chrs) 10 and 18 with broad-spectrum resistance to the three nematodes present in this germplasm. Haplotype and copy number variation analyses of SCN resistance QTL indicated that PI 567305 has a different haplotype, which is associated with likely a unique SCN resistance mechanism different from Peking- or PI 88788-type resistance. The evaluations of both Infinium Beadchip- and GBS-based genotyping technologies provided comprehensive insights for researchers to choose a cost-effective and efficient platform for QTL mapping and for other genomic studies in soybeans.
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Affiliation(s)
- T D Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - H Sonah
- Département de Phytologie, Faculté Des Sciences de L'Agriculture Et de L'Alimentation, Centre de Recherche en Horticulture, Université Laval, Québec, Canada
- National Agri-Food Biotechnology Institute, Sector 81, Mohali-140306, P.O. Manauli, Punjab, India
| | - G Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance (IGCAST), Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - C Meinhardt
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - M Usovsky
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - K S Kim
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
- LG Chem-FarmHannong, Ltd, Daejeon, 34115, Republic of Korea
| | - F Belzile
- Département de Phytologie, Université Laval, Pavillon Charles-Eugène Marchand 1030, Avenue de la Médecine, Québec, Canada
| | - Z Li
- Institute of Plant Breeding, Genetics, Genomics and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - R Robbins
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA
| | - J G Shannon
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - H T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
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Tai L, Wang HJ, Xu XJ, Sun WH, Ju L, Liu WT, Li WQ, Sun J, Chen KM. Pre-harvest sprouting in cereals: genetic and biochemical mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2857-2876. [PMID: 33471899 DOI: 10.1093/jxb/erab024] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/18/2021] [Indexed: 05/22/2023]
Abstract
With the growth of the global population and the increasing frequency of natural disasters, crop yields must be steadily increased to enhance human adaptability to risks. Pre-harvest sprouting (PHS), a term mainly used to describe the phenomenon in which grains germinate on the mother plant directly before harvest, is a serious global problem for agricultural production. After domestication, the dormancy level of cultivated crops was generally lower than that of their wild ancestors. Although the shortened dormancy period likely improved the industrial performance of cereals such as wheat, barley, rice, and maize, the excessive germination rate has caused frequent PHS in areas with higher rainfall, resulting in great economic losses. Here, we systematically review the causes of PHS and its consequences, the major indicators and methods for PHS assessment, and emphasize the biological significance of PHS in crop production. Wheat quantitative trait loci functioning in the control of PHS are also comprehensively summarized in a meta-analysis. Finally, we use Arabidopsis as a model plant to develop more complete PHS regulatory networks for wheat. The integration of this information is conducive to the development of custom-made cultivated lines suitable for different demands and regions, and is of great significance for improving crop yields and economic benefits.
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Affiliation(s)
- Li Tai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hong-Jin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiao-Jing Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wei-Hang Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lan Ju
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
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9
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McGinty EM, Murphy KM, Hauvermale AL. Seed Dormancy and Preharvest Sprouting in Quinoa ( Chenopodium quinoa Willd.). PLANTS (BASEL, SWITZERLAND) 2021; 10:458. [PMID: 33670959 PMCID: PMC7997350 DOI: 10.3390/plants10030458] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 01/13/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a culturally significant staple food source that has been grown for thousands of years in South America. Due to its natural drought and salinity tolerance, quinoa has emerged as an agronomically important crop for production in marginal soils, in highly variable climates, and as part of diverse crop rotations. Primary areas of quinoa research have focused on improving resistance to abiotic stresses and disease, improving yields, and increasing nutrition. However, an evolving issue impacting quinoa seed end-use quality is preharvest sprouting (PHS), which is when seeds with little to no dormancy experience a rain event prior to harvest and sprout on the panicle. Far less is understood about the mechanisms that regulate quinoa seed dormancy and seed viability. This review will cover topics including seed dormancy, orthodox and unorthodox dormancy programs, desiccation sensitivity, environmental and hormonal mechanisms that regulate seed dormancy, and breeding and non-breeding strategies for enhancing resistance to PHS in quinoa.
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Affiliation(s)
- Emma M. McGinty
- The School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, WA 99164, USA;
| | - Kevin M. Murphy
- Department of Crop and Soil Science, Washington State University, Pullman, WA 99164, USA;
| | - Amber L. Hauvermale
- Department of Crop and Soil Science, Washington State University, Pullman, WA 99164, USA;
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10
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Park YJ, Lee MN, Noh JK, Noh ES, Kang JH, Park JY, Kim EM. Classification of Takifugu rubripes, T. chinensis and T. pseudommus by genotyping-by-sequencing. PLoS One 2020; 15:e0236483. [PMID: 32853203 PMCID: PMC7451653 DOI: 10.1371/journal.pone.0236483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 11/18/2022] Open
Abstract
Takifugu rubripes is more expensive than other species of the genus because of its high protein content and special flavor. However, it is easily confused with imported T. chinensis and T. pseudommus because they have similar morphological characteristics. We identified single nucleotide polymorphism (SNP) markers of T. rubripes by genotyping-by-sequencing (GBS) and evaluated their ability to distinguish among T. rubripes, T. chinensis, and T. pseudommus. In all, 18 polymorphic SNPs were subjected to phylogenetic analyses of the three Takifugu species. Additionally, we subjected a second set of samples to Sanger sequencing to verify that the polymorphic SNPs could be used to evaluate the genetic variation among the three Takifugu species. A phylogenetic tree that included the analyzed sequence of set A, which is referred to as the reference sequence, and a validation sequence of set B with 18 SNPs were produced. Based on this phylogenetic tree and STRUCTURE analyses, T. rubripes, T. chinensis and T. pseudommus have low genetic variation and should be considered the same gene pool. Our findings suggest that further studies are needed to estimate the genetic association of the three Takifugu species.
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Affiliation(s)
- Yeon Jung Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Mi Nan Lee
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Jae Koo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Jung Ha Kang
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
- * E-mail:
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11
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Khedikar Y, Clarke WE, Chen L, Higgins EE, Kagale S, Koh CS, Bennett R, Parkin IAP. Narrow genetic base shapes population structure and linkage disequilibrium in an industrial oilseed crop, Brassica carinata A. Braun. Sci Rep 2020; 10:12629. [PMID: 32724070 PMCID: PMC7387349 DOI: 10.1038/s41598-020-69255-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022] Open
Abstract
Ethiopian mustard (Brassica carinata A. Braun) is an emerging sustainable source of vegetable oil, in particular for the biofuel industry. The present study exploited genome assemblies of the Brassica diploids, Brassica nigra and Brassica oleracea, to discover over 10,000 genome-wide SNPs using genotype by sequencing of 620 B. carinata lines. The analyses revealed a SNP frequency of one every 91.7 kb, a heterozygosity level of 0.30, nucleotide diversity levels of 1.31 × 10-05, and the first five principal components captured only 13% molecular variation, indicating low levels of genetic diversity among the B. carinata collection. Genome bias was observed, with greater SNP density found on the B subgenome. The 620 lines clustered into two distinct sub-populations (SP1 and SP2) with the majority of accessions (88%) clustered in SP1 with those from Ethiopia, the presumed centre of origin. SP2 was distinguished by a collection of breeding lines, implicating targeted selection in creating population structure. Two selective sweep regions on B3 and B8 were detected, which harbour genes involved in fatty acid and aliphatic glucosinolate biosynthesis, respectively. The assessment of genetic diversity, population structure, and LD in the global B. carinata collection provides critical information to assist future crop improvement.
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Affiliation(s)
- Yogendra Khedikar
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Wayne E Clarke
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Lifeng Chen
- Agrisoma Biosciences Inc., 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada
| | - Sateesh Kagale
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Chu Shin Koh
- Global Institute of Food Security, Saskatoon, SK, Canada
| | - Rick Bennett
- Agrisoma Biosciences Inc., 110 Gymnasium Place, Saskatoon, SK, Canada
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada.
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Zhang B, Jia L, He X, Chen C, Liu H, Liu K, Zhao N, Bao B. Large scale SNP unearthing and genetic architecture analysis in sea-captured and cultured populations of Cynoglossus semilaevis. Genomics 2020; 112:3238-3246. [PMID: 32531446 DOI: 10.1016/j.ygeno.2020.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/09/2020] [Accepted: 06/06/2020] [Indexed: 01/07/2023]
Abstract
Knowledge on population structure and genetic diversity is a focal point for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Here we used the GBS approach for the genome-wide identification of SNPs in a collection of Cynoglossus semilaevis and for the assessment of the level of genetic diversity in C. semilaevis genotypes. GBS analysis generated a total of 55.12 Gb high-quality sequence data, with an average of 0.63 Gb per sample. The total number of SNP markers was 563, 109. In order to explore the genetic diversity of C. semilaevis and to select a minimal core set representing most of the total genetic variation with minimum redundancy, C. semilaevis sequences were analyzed using high quality SNPs. Based on hierarchical clustering, it was possible to divide the collection into 2 clusters. The marine fishing populations were clustered and clearly separated from the cultured populations, and the cultured populations from Hebei was also distinct from the other two local populations. These analyses showed that genotypes were clustered based on species-related features. Differential significant SNPs were also captured and validated by GBS and SNaPshot, with linkage disequilibrium and haplotype analysis, seven SNPs have been confirmed to have obvious differentiation in two populations, which may be used as the characteristic evaluation sites of sea-captured and cultured Cynoglossus semilaevis populations. And SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs. These differential SNPs could be also employed as the characteristic evaluation sites of sea-captured and cultured Cynoglossus semilaevis populations in future.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China;International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Lei Jia
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Xiaoxu He
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Chunxiu Chen
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Hao Liu
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Haolinsaiao Biotechnology Co, Ltd, Tianjin, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China;International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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13
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Gupta PK, Balyan HS, Sharma S, Kumar R. Genetics of yield, abiotic stress tolerance and biofortification in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1569-1602. [PMID: 32253477 DOI: 10.1007/s00122-020-03583-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 05/18/2023]
Abstract
A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.
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Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India.
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
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Wu X, Alexander LW. Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla. HORTICULTURE RESEARCH 2020; 7:27. [PMID: 32140236 PMCID: PMC7049302 DOI: 10.1038/s41438-020-0255-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/31/2019] [Accepted: 01/04/2020] [Indexed: 05/28/2023]
Abstract
Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophylla L.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteen H. macrophylla cultivars. The SNP was investigated in 341 F1 progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ 2 = 0.12; P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.
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Affiliation(s)
- Xingbo Wu
- Oak Ridge Institute of Science and Technology, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN USA
| | - Lisa W. Alexander
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Otis L. Floyd Nursery Research Center, 472 Cadillac Lane, McMinnville, TN USA
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15
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Bernardo A, St. Amand P, Le HQ, Su Z, Bai G. Multiplex restriction amplicon sequencing: a novel next-generation sequencing-based marker platform for high-throughput genotyping. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:254-265. [PMID: 31199572 PMCID: PMC6920337 DOI: 10.1111/pbi.13192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 05/31/2023]
Abstract
To enable rapid selection of traits in marker-assisted breeding, markers must be technically simple, low-cost, high-throughput and randomly distributed in a genome. We developed such a technology, designated as Multiplex Restriction Amplicon Sequencing (MRASeq), which reduces genome complexity by polymerase chain reaction (PCR) amplification of amplicons flanked by restriction sites. The first PCR primers contain restriction site sequences at 3'-ends, preceded by 6-10 bases of specific or degenerate nucleotide sequences and then by a unique M13-tail sequence which serves as a binding site for a second PCR that adds sequencing primers and barcodes to allow sample multiplexing for sequencing. The sequences of restriction sites and adjacent nucleotides can be altered to suit different species. Physical mapping of MRASeq SNPs from a biparental population of allohexaploid wheat (Triticum aestivum L.) showed a random distribution of SNPs across the genome. MRASeq generated thousands of SNPs from a wheat biparental population and natural populations of wheat and barley (Hordeum vulgare L.). This novel, next-generation sequencing-based genotyping platform can be used for linkage mapping to screen quantitative trait loci (QTL), background selection in breeding and many other genetics and breeding applications of various species.
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Affiliation(s)
- Amy Bernardo
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Paul St. Amand
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
| | - Ha Quang Le
- Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | - Zhenqi Su
- Department of AgronomyKansas State UniversityManhattanKSUSA
- China Agricultural UniversityBeijingChina
| | - Guihua Bai
- Hard Winter Wheat Genetics Research UnitUSDA‐ARSManhattanKSUSA
- Department of AgronomyKansas State UniversityManhattanKSUSA
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16
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Zhu Y, Wang S, Wei W, Xie H, Liu K, Zhang C, Wu Z, Jiang H, Cao J, Zhao L, Lu J, Zhang H, Chang C, Xia X, Xiao S, Ma C. Genome-wide association study of pre-harvest sprouting tolerance using a 90K SNP array in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2947-2963. [PMID: 31324930 DOI: 10.1007/s00122-019-03398-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 06/29/2019] [Accepted: 07/11/2019] [Indexed: 05/06/2023]
Abstract
Three major loci for pre-harvest sprouting tolerance (PHST) were mapped on chromosomes 1AL, 3BS, and 6BL, and two CAPS and one dCAPS markers were validated. Sixteen lines with favorable alleles and increased PHST were identified. Pre-harvest sprouting (PHS) significantly affects wheat grain yield and quality. In the present study, the PHS tolerance (PHST) of 192 wheat varieties (lines) was evaluated by assessment of field sprouting, seed germination index, and period of dormancy in different environments. A high-density Illumina iSelect 90K SNP array was used to genotype the panel. A genome-wide association study (GWAS) based on single- and multi-locus mixed linear models was used to detect loci for PHST. The single-locus model identified 23 loci for PHST (P < 0.0001) and explained 6.0-18.9% of the phenotypic variance. Twenty loci were consistent with known quantitative trait loci (QTLs). Three single-nucleotide polymorphism markers closely linked with three major loci (Qphs.ahau-1A, Qphs.ahau-3B, and Qphs.ahau-6B) on chromosomes 1AL, 3BS, and 6BL, respectively, were converted to two cleaved amplified polymorphic sequences (CAPS) and one derived-CAPS markers, and validated in 374 wheat varieties (lines). The CAPS marker EX06323 for Qphs.ahau-6B co-segregated with a novel major QTL underlying PHST in a recombinant inbred line population raised from the cross Jing 411 × Wanxianbaimaizi. Linear regression showed a clear dependence of PHST on the number of favorable alleles. Sixteen varieties showing an elevated degree of PHST were identified and harbored more than 16 favorable alleles. The multi-locus model detected 39 marker-trait associations for PHST (P < 0.0001), of which five may be novel. Six loci common to the two models were identified. The combination of the two GWAS methods contributes to efficient dissection of the complex genetic mechanism of PHST.
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Affiliation(s)
- Yulei Zhu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Shengxing Wang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Wenxin Wei
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Hongyong Xie
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Kai Liu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Can Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Zengyun Wu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Hao Jiang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Jiajia Cao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Liangxia Zhao
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
| | - Haiping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China.
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China.
| | - Xianchun Xia
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Shihe Xiao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China
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17
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Zhu S, Niu E, Shi A, Mou B. Genetic Diversity Analysis of Olive Germplasm ( Olea europaea L.) With Genotyping-by-Sequencing Technology. Front Genet 2019; 10:755. [PMID: 31497033 PMCID: PMC6712157 DOI: 10.3389/fgene.2019.00755] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
Olive (Olea europaea L.) is a very important edible oil crop and has been cultivated for about 4,000 years in the Mediterranean area. Due to its nutritional and economic importance, researches on germplasm characterization received extensive attention. In this study, using the genotyping-by-sequencing (GBS) technology, we carried out genetic diversity analysis on 57 olive cultivars with different geographical origins. In total, 73,482 high-quality single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) > 5%, call rate > 50%, and heterozygosity rate < 10% were obtained at the whole genome level. Genetic structure and phylogenetic analysis showed that the 57 olive cultivars could be classified into two groups (Group I and Group II). No clear geographical distributions of cultivars were observed generally between the two groups. The average nucleotide diversities (π) specific for Group I and Group II were 0.317 and 0.305. The fixation index (FST) between Group I and Group II was 0.033. In Group II, cultivars could be further divided into two subgroups (Group IIa and Group IIb), which seem to be associated with their fruit sizes. The five Chinese-bred cultivars were all clustered in Group II, showing a closer genetic relationship with those from the central Mediterranean region and limited genetic background. It is therefore necessary for Chinese olive breeding programs to incorporate other genetic basis by utilizing germplasm from the other regions particularly from the east Mediterranean region as breeding parents. The results showed that GBS is an effective marker choice for cultivar characterization and genetic diversity analysis in olive and will help us better understand the genetic backgrounds of the crop.
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Affiliation(s)
- Shenlong Zhu
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Erli Niu
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Beiquan Mou
- U.S. Department of Agriculture, Agricultural Research Service, Salinas, CA, United States
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18
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Wang X, Liu H, Liu G, Mia MS, Siddique KHM, Yan G. Phenotypic and genotypic characterization of near-isogenic lines targeting a major 4BL QTL responsible for pre-harvest sprouting in wheat. BMC PLANT BIOLOGY 2019; 19:348. [PMID: 31399046 PMCID: PMC6688225 DOI: 10.1186/s12870-019-1961-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/06/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Resistance to pre-harvest sprouting (PHS) is one of the major objectives in wheat breeding programs. However, the complex quantitative nature of this trait presents challenges when breeding for PHS resistance. Characterization of PHS using near-isogenic lines (NILs) targeting major quantitative trait locus/loci (QTL/QTLs) can be an effective strategy for the identification of responsible genes and underlying mechanisms. RESULTS In this study, multiple pairs of NILs were developed and confirmed for a major QTL located on the 4BL chromosome arm that contributes to PHS resistance in wheat, using a combined heterogeneous inbred family method and a fast generation cycling system. Phenotypic characterization of these confirmed NILs revealed significant differences in PHS resistance between the isolines, where the presence of the resistant allele increased the resistance to sprouting on spikes by 54.0-81.9% (average 70.8%) and reduced seed germination by 59.4-70.5% (average 66.2%). The 90 K SNP genotyping assay on the confirmed NIL pairs identified eight SNPs on 4BL, associated with five candidate genes; two of the candidate genes were related to seed dormancy. Agronomic traits in the NIL pairs were investigated; both plant height and grain number per spike were positively correlated with PHS susceptibility. CONCLUSIONS This study confirmed multiple pairs of NILs and identified SNPs between PHS isolines, which are valuable resources for further fine-mapping of this locus to clone the major genes for PHS resistance and investigate the possible functional regulation of these genes on important agronomic traits, such as plant height and grain number per spike.
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Affiliation(s)
- Xingyi Wang
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Guannan Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Md Sultan Mia
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Plant Breeding Division, Bangladesh Agricultural Research Institute, Joydebpur, Gazipur, 1701, Bangladesh
| | - Kadambot H M Siddique
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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19
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Zuo J, Lin CT, Cao H, Chen F, Liu Y, Liu J. Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.). PLANTA 2019; 250:187-198. [PMID: 30972483 DOI: 10.1007/s00425-019-03164-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 04/06/2019] [Indexed: 05/06/2023]
Abstract
Totally, 23 and 26 loci for the first count germination ratio and the final germination ratio were detected by quantitative trait loci (QTL) mapping and association mapping, respectively, which could be used to facilitate wheat pre-harvest sprouting breeding. Weak dormancy can cause pre-harvest sprouting in seeds of common wheat which significantly reduces grain yield. In this study, both quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) were used to identify loci controlling seed dormancy. The analyses were based on a recombinant inbred line population derived from Zhou 8425B/Chinese Spring cross and 166 common wheat accessions. Inclusive composite interval mapping detected 8 QTL, while 45 loci were identified in the 166 wheat accessions by GWAS. Among these, four loci (Qbifcgr.cas-3AS/Qfcgr.cas-3AS, Qbifcgr.cas-6AL.1/Qfcgr.cas-6AL.1, Qbifcgr.cas-7BL.2/Qfcgr.cas-7BL.2, and Qbigr.cas-3DL/Qgr.cas-3DL) were detected in both QTL mapping and GWAS. In addition, 41 loci co-located with QTL reported previously, whereas 8 loci (Qfcgr.cas-5AL, Qfcgr.cas-6DS, Qfcgr.cas-7AS, Qgr.cas-3DS.1, Qgr.cas-3DS.2, Qbigr.cas-3DL/Qgr.cas-3DL, Qgr.cas-4B, and Qgr.cas-5A) were likely to be new. Linear regression showed the first count germination ratio or the final germination ratio reduced while multiple favorable alleles increased. It is suggested that QTL pyramiding was effective to reduce pre-harvest sprouting risk. This study could enrich the research on pre-harvest sprouting and provide valuable information of marker exploration for wheat breeding programs.
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Affiliation(s)
- Jinghong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Science, Beijing, China
| | - Chih-Ta Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- College of Life Science, University of Chinese Academy of Science, Beijing, China.
| | - Jindong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
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20
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Vetch JM, Stougaard RN, Martin JM, Giroux MJ. Review: Revealing the genetic mechanisms of pre-harvest sprouting in hexaploid wheat (Triticum aestivum L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:180-185. [PMID: 30824050 DOI: 10.1016/j.plantsci.2019.01.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/21/2018] [Accepted: 01/07/2019] [Indexed: 05/06/2023]
Abstract
Pre-harvest sprouting (PHS) of wheat (Triticum aestivum L.) is an important phenomenon that results in weather dependent reductions in grain yield and quality across the globe. Due to the large annual losses, breeding PHS resistant varieties is of great importance. Many quantitative trait loci have been associated with PHS and a number of specific genes have been proven to impact PHS. TaPHS1, TaMKK3, Tamyb10, and TaVp1 have been shown to have a large impact on PHS susceptibility while many other genes such as TaSdr, TaQSd, and TaDOG1 have been shown to account for smaller, but significant, proportions of variation. These advances in understanding the genetics behind PHS are making molecular selection and loci stacking viable methods for affecting this quantitative trait. The current review article serves to provide a brief synthesis of recent advances regarding PHS, as well as provide unique insight into the genetic mechanisms governing PHS in bread wheat.
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Affiliation(s)
- Justin M Vetch
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| | - Robert N Stougaard
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA; College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| | - John M Martin
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| | - Michael J Giroux
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA.
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21
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Unraveling Molecular and Genetic Studies of Wheat (Triticum aestivum L.) Resistance against Factors Causing Pre-Harvest Sprouting. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9030117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pre-harvest sprouting (PHS) is one of the most important factors having adverse effects on yield and grain quality all over the world, particularly in wet harvest conditions. PHS is controlled by both genetic and environmental factors and the interaction of these factors. Breeding varieties with high PHS resistance have important implications for reducing yield loss and improving grain quality. The rapid advancements in the wheat genomic database along with transcriptomic and proteomic technologies have broadened our knowledge for understanding the regulatory mechanism of PHS resistance at transcriptomic and post-transcriptomic levels. In this review, we have described in detail the recent advancements on factors influencing PHS resistance, including grain color, seed dormancy, α-amylase activity, plant hormones (especially abscisic acid and gibberellin), and QTL/genes, which are useful for mining new PHS-resistant genes and developing new molecular markers for multi-gene pyramiding breeding of wheat PHS resistance, and understanding the complicated regulatory mechanism of PHS resistance.
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22
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Shao M, Bai G, Rife TW, Poland J, Lin M, Liu S, Chen H, Kumssa T, Fritz A, Trick H, Li Y, Zhang G. QTL mapping of pre-harvest sprouting resistance in a white wheat cultivar Danby. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1683-1697. [PMID: 29860625 DOI: 10.1007/s00122-018-3107-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 05/02/2018] [Indexed: 05/06/2023]
Abstract
One major and three minor QTLs for resistance to pre-harvest sprouting (PHS) were identified from a white wheat variety "Danby." The major QTL on chromosome 3A is TaPHS1, and the sequence variation in its promoter region was responsible for the PHS resistance. Additive × additive effects were detected between two minor QTLs on chromosomes 3B and 5A, which can greatly enhance the PHS resistance. Pre-harvest sprouting (PHS) causes significant losses in yield and quality in wheat. White wheat is usually more susceptible to PHS than red wheat. Therefore, the use of none grain color-related PHS resistance quantitative trait loci (QTLs) is essential for the improvement in PHS resistance in white wheat. To identify PHS resistance QTLs in the white wheat cultivar "Danby" and determine their effects, a doubled haploid population derived from a cross of Danby × "Tiger" was genotyped using genotyping-by-sequencing markers and phenotyped for PHS resistance in two greenhouse and one field experiments. One major QTL corresponding to a previously cloned gene, TaPHS1, was consistently detected on the chromosome arm 3AS in all three experiments and explained 21.6-41.0% of the phenotypic variations. A SNP (SNP-222) in the promoter of TaPHS1 co-segregated with PHS in this mapping population and was also significantly associated with PHS in an association panel. Gene sequence comparison and gene expression analysis further confirmed that SNP-222 is most likely the causal mutation in TaPHS1 for PHS resistance in Danby in this study. In addition, two stable minor QTLs on chromosome arms 3BS and 5AL were detected in two experiments with allele effects consistently contributed by Danby, while one minor QTL on 2AS was detected in two environments with contradicted allelic effects. The two stable minor QTLs showed significant additive × additive effects. The results demonstrated that pyramiding those three QTLs using breeder-friendly KASP markers developed in this study could greatly improve PHS resistance in white wheat.
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Affiliation(s)
- Mingqin Shao
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- USDA-ARS, Plant Science and Entomology Research Unit, Manhattan, KS, 66506, USA
| | - Trevor W Rife
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Meng Lin
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Shubing Liu
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Hui Chen
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Tadele Kumssa
- Agricultural Research Center-Hays, Kansas State University, Hays, KS, 67601, USA
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Harold Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yan Li
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Guorong Zhang
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
- Agricultural Research Center-Hays, Kansas State University, Hays, KS, 67601, USA.
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23
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Li CX, Xu WG, Guo R, Zhang JZ, Qi XL, Hu L, Zhao MZ. Molecular marker assisted breeding and genome composition analysis of Zhengmai 7698, an elite winter wheat cultivar. Sci Rep 2018; 8:322. [PMID: 29321647 PMCID: PMC5762757 DOI: 10.1038/s41598-017-18726-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 12/15/2017] [Indexed: 11/09/2022] Open
Abstract
Zhengmai 7698 is an elite winter wheat variety widely cultivated in the Southern regions of the Yellow-Huai River Valley of China. Here, we report the molecular markers used for breeding Zhengmai 7698 and the genome composition of this cultivar revealed using genome-wide SNPs. A total of 26 DNA markers derived from the genes controlling gluten protein quality, grain hardness, flour color, disease resistance, or pre-harvesting sprouting resistance were used during breeding. Consequently, Zhengmai 7698 had strong gluten, high grain hardness index, white flour color, and high levels of resistance to powdery mildew, stripe rust infections, and pre-harvesting sprouting. Using genome complexity reduction, 28,996 high-quality SNPs distributed on 21 wheat chromosomes were identified among Zhengmai 7698 and its three parental lines (4B269, Zhengmai 9405 and Zhoumai 16). Zhengmai 7698 shared 12,776, 14,411 and 16,085 SNPs with 4B269, Zhengmai 9405 and Zhoumai 16, respectively. Thus, the contributions of 4B269, Zhengmai 9405 and Zhoumai 16 to the genome of Zhengmai 7698 were comparable. Interestingly, Zhengmai 7698 had 307 unique SNPs that are absent in all three parents. We suggest that molecular markers facilitate selection of a wheat cultivar with multiple elite traits. Analysis of genome composition with SNPs may provide useful clues for further dissecting the genetic basis of improved wheat performance.
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Affiliation(s)
- Chun-Xin Li
- Molecular Breeding Laboratory, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Wei-Gang Xu
- Molecular Breeding Laboratory, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
| | - Rui Guo
- Molecular Breeding Laboratory, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Jian-Zhou Zhang
- Molecular Breeding Laboratory, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Xue-Li Qi
- Molecular Breeding Laboratory, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Lin Hu
- Molecular Breeding Laboratory, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Ming-Zhong Zhao
- Molecular Breeding Laboratory, Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
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24
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Alam Z, Roncal J, Peña-Castillo L. Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea. BMC Genomics 2018; 19:4. [PMID: 29291734 PMCID: PMC5748963 DOI: 10.1186/s12864-017-4396-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/19/2017] [Indexed: 12/31/2022] Open
Abstract
Background Lingonberry (Vaccinium vitis-idaea L.), one of the least studied fruit crops in the Ericaceae family, has a dramatically increased worldwide demand due to its numerous health benefits. Genetic markers can facilitate the selection of berries with desirable climatic adaptations, agronomic and nutritious characteristics to improve cultivation programs. However, no genomic resources are available for this species. Results We used Genotyping-by-Sequencing (GBS) to analyze the genetic variation of 56 lingonberry samples from across Newfoundland and Labrador, Canada. To elucidate a potential adaptation to environmental conditions we searched for genotype-environment associations by applying three distinct approaches to screen the identified single nucleotide polymorphisms (SNPs) for correlation with six environmental variables. We also searched for an association between the identified SNPs and two phenotypic traits: the total phenolic content (TPC) and antioxidant capacity (AC) of fruit. We identified 1586 high-quality putative SNPs using the UNEAK pipeline available in TASSEL. We found 132 SNPs likely associated with at least one of the environmental or phenotypic variables. To obtain insights on the function of the genomic sequences containing the SNPs likely to be associated with the environmental or phenotypic variables, we performed a sequence-based functional annotation and identified homologous protein-coding sequences with functional roles related to abiotic stress response, pathogen defense, RNA metabolism, and, most interestingly, phenolic compound biosynthesis. Conclusions The putative SNPs discovered are the first genomic resource for lingonberry. This resource might prove useful in high-density quantitative trait locus analysis, and association mapping. The identified candidate genes containing the SNPs need further studies on their potential role in local adaptation of lingonberry. Altogether, the present study provides new resources that can be used to breed for desirable traits in lingonberry. Electronic supplementary material The online version of this article (10.1186/s12864-017-4396-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zobayer Alam
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada
| | - Julissa Roncal
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
| | - Lourdes Peña-Castillo
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.,Department of Computer Science, Memorial University of Newfoundland, St. John's, NL, A1B 3X5, Canada
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25
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Hussain W, Baenziger PS, Belamkar V, Guttieri MJ, Venegas JP, Easterly A, Sallam A, Poland J. Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat. Sci Rep 2017; 7:16394. [PMID: 29180623 PMCID: PMC5703991 DOI: 10.1038/s41598-017-16006-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022] Open
Abstract
Winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) were used to develop a recombinant inbred population with future goals of identifying genomic regions associated with drought tolerance. To precisely map genomic regions, high-density linkage maps are a prerequisite. In this study genotyping-by- sequencing (GBS) was used to construct the high-density linkage map. The map contained 3,641 markers distributed on 21 chromosomes and spanned 1,959 cM with an average distance of 1.8 cM between markers. The constructed linkage map revealed strong collinearity in marker order across 21 chromosomes with POPSEQ-v2.0, which was based on a high-density linkage map. The reliability of the linkage map for QTL mapping was demonstrated by co-localizing the genes to previously mapped genomic regions for two highly heritable traits, chaff color, and leaf cuticular wax. Applicability of linkage map for QTL mapping of three quantitative traits, flag leaf length, width, and area, identified 21 QTLs in four environments, and QTL expression varied across the environments. Two major stable QTLs, one each for flag leaf length (Qfll.hww-7A) and flag leaf width (Qflw.hww-5A) were identified. The map constructed will facilitate QTL and fine mapping of quantitative traits, map-based cloning, comparative mapping, and in marker-assisted wheat breeding endeavors.
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Affiliation(s)
- Waseem Hussain
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - P Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Mary J Guttieri
- USDA, Agricultural Research Service, Center for Grain and Animal Health Research, Hard Winter Wheat Genetics Research Unit, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - Jorge P Venegas
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Amanda Easterly
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Ahmed Sallam
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526, Assiut, Egypt
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
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26
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Wu X, Blair MW. Diversity in Grain Amaranths and Relatives Distinguished by Genotyping by Sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2017; 8:1960. [PMID: 29204149 PMCID: PMC5698268 DOI: 10.3389/fpls.2017.01960] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/31/2017] [Indexed: 05/26/2023]
Abstract
The genotyping by sequencing (GBS) method has become a molecular marker technology of choice for many crop plants because of its simultaneous discovery and evaluation of a large number of single nucleotide polymorphisms (SNPs) and utility for germplasm characterization. Genome representation and complexity reduction are the basis for GBS fingerprinting and can vary by species based on genome size and other sequence characteristics. Grain amaranths are a set of three species that were domesticated in the New World to be high protein, pseudo-cereal grain crops. The goal of this research was to employ the GBS technique for diversity evaluation in grain amaranth accessions and close relatives from six Amaranthus species and determine genetic differences and similarities between groupings. A total of 10,668 SNPs were discovered in 94 amaranth accessions with ApeKI complexity reduction and 10X genome coverage Illumina sequencing. The majority of the SNPs were species specific with 4,568 and 3,082 for the two grain amaranths originating in Central America Amaranthus cruentus and A. hypochondriacus and 3,284 found amongst both A. caudatus, originally domesticated in South America, and its close relative, A. quitensis. The distance matrix based on shared alleles provided information on the close relationships of the two cultivated Central American species with each other and of the wild and cultivated South American species with each other, as distinguished from the outgroup with two wild species, A. powellii and A. retroflexus. The GBS data also distinguished admixture between each pair of species and the geographical origins and seed colors of the accessions. The SNPs we discovered here can be used for marker development for future amaranth study.
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Affiliation(s)
| | - Matthew W. Blair
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
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27
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Lin Y, Liu S, Liu Y, Liu Y, Chen G, Xu J, Deng M, Jiang Q, Wei Y, Lu Y, Zheng Y. Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents. Genet Mol Biol 2017; 40:620-629. [PMID: 28696481 PMCID: PMC5596365 DOI: 10.1590/1678-4685-gmb-2016-0207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 02/28/2017] [Indexed: 12/23/2022] Open
Abstract
Pre-harvest sprouting (PHS) is a major abiotic factor affecting grain weight and
quality, and is caused by an early break in seed dormancy. Association mapping (AM)
is used to detect correlations between phenotypes and genotypes based on linkage
disequilibrium (LD) in wheat breeding programs. We evaluated seed dormancy in 80
Chinese wheat founder parents in five environments and performed a genome-wide
association study using 6,057 markers, including 93 simple sequence repeat (SSR),
1,472 diversity array technology (DArT), and 4,492 single nucleotide polymorphism
(SNP) markers. The general linear model (GLM) and the mixed linear model (MLM) were
used in this study, and two significant markers (tPt-7980 and
wPt-6457) were identified. Both markers were located on
Chromosome 1B, with wPt-6457 having been identified in a previously
reported chromosomal position. The significantly associated loci contain essential
information for cloning genes related to resistance to PHS and can be used in wheat
breeding programs.
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Affiliation(s)
- Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Shihang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yujiao Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
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28
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Chen W, Hou L, Zhang Z, Pang X, Li Y. Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:575. [PMID: 28458680 PMCID: PMC5394126 DOI: 10.3389/fpls.2017.00575] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 03/30/2017] [Indexed: 05/24/2023]
Abstract
Chinese jujube (Ziziphus jujuba Mill) is an economically important fruit species native to China with high nutritious and medicinal value. Genotyping-by-sequencing was used to detect and genotype single nucleotide polymorphisms (SNPs) in a core collection of 150 Chinese jujube accessions and further to characterize their genetic diversity, population structure, and linkage disequilibrium (LD). A total of 4,680 high-quality SNPs were identified, of which 38 sets of tri-allelic SNPs were detected. The average polymorphism information content (PIC) values based on bi-allelic SNPs and tri-allelic SNPs were 0.27 and 0.38, respectively. STRUCTURE and principal coordinate analyses based on SNPs revealed that the 150 accessions could be clustered into two groups. However, neighbor-joining trees indicated the accessions should be grouped into three major clusters. Our data confirm that the resolving power for genetic diversity was similar for the SSRs and SNPs. In contrast, regarding population structure, the resolving power was higher for SSRs than for SNPs. The LD pattern in Chinese jujube was investigated for the first time. We observed a relatively rapid LD decay with a short range (∼10 kb) for all pseudo-chromosomes and for individual pseudo-chromosomes. Our findings provide important information for future genome-wide association analyses and marker-assisted selective breeding of Chinese jujube.
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Affiliation(s)
- Wu Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Lu Hou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Zhiyong Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry UniversityBeijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijing, China
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29
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Pasam RK, Bansal U, Daetwyler HD, Forrest KL, Wong D, Petkowski J, Willey N, Randhawa M, Chhetri M, Miah H, Tibbits J, Bariana H, Hayden MJ. Detection and validation of genomic regions associated with resistance to rust diseases in a worldwide hexaploid wheat landrace collection using BayesR and mixed linear model approaches. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:777-793. [PMID: 28255670 DOI: 10.1007/s00122-016-2851-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/28/2016] [Indexed: 05/26/2023]
Abstract
BayesR and MLM association mapping approaches in common wheat landraces were used to identify genomic regions conferring resistance to Yr, Lr, and Sr diseases. Deployment of rust resistant cultivars is the most economically effective and environmentally friendly strategy to control rust diseases in wheat. However, the highly evolving nature of wheat rust pathogens demands continued identification, characterization, and transfer of new resistance alleles into new varieties to achieve durable rust control. In this study, we undertook genome-wide association studies (GWAS) using a mixed linear model (MLM) and the Bayesian multilocus method (BayesR) to identify QTL contributing to leaf rust (Lr), stem rust (Sr), and stripe rust (Yr) resistance. Our study included 676 pre-Green Revolution common wheat landrace accessions collected in the 1920-1930s by A.E. Watkins. We show that both methods produce similar results, although BayesR had reduced background signals, enabling clearer definition of QTL positions. For the three rust diseases, we found 5 (Lr), 14 (Yr), and 11 (Sr) SNPs significant in both methods above stringent false-discovery rate thresholds. Validation of marker-trait associations with known rust QTL from the literature and additional genotypic and phenotypic characterisation of biparental populations showed that the landraces harbour both previously mapped and potentially new genes for resistance to rust diseases. Our results demonstrate that pre-Green Revolution landraces provide a rich source of genes to increase genetic diversity for rust resistance to facilitate the development of wheat varieties with more durable rust resistance.
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Affiliation(s)
- Raj K Pasam
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Urmil Bansal
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
| | - Hans D Daetwyler
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Kerrie L Forrest
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Debbie Wong
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Joanna Petkowski
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Nicholas Willey
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
- Dow AgroSciences Australia Ltd, Unit 12A, 84 Barnes Street, Tamworth, NSW, 2340, Australia
| | - Mandeep Randhawa
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, México, C.P. 56237, Mexico
| | - Mumta Chhetri
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
| | - Hanif Miah
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia
| | - Josquin Tibbits
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Harbans Bariana
- Faculty of Agriculture and Environment, Plant Breeding Institute-Cobbitty, The University of Sydney, PMB4011, Narellan, NSW, 2567, Australia.
| | - Matthew J Hayden
- Department of Economic Development, Jobs, Transport and Recourses, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
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30
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Furuta T, Ashikari M, Jena KK, Doi K, Reuscher S. Adapting Genotyping-by-Sequencing for Rice F2 Populations. G3 (BETHESDA, MD.) 2017; 7:881-893. [PMID: 28082325 PMCID: PMC5345719 DOI: 10.1534/g3.116.038190] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/09/2017] [Indexed: 12/30/2022]
Abstract
Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536 cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.
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Affiliation(s)
- Tomoyuki Furuta
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
| | - Kshirod K Jena
- Plant Breeding Division, International Rice Research Institute, 1301 Manila, Philippines
| | - Kazuyuki Doi
- Associated Field Science and Research Center, Nagoya University, 470-0151, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, 464-8601, Japan
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Celik I, Gurbuz N, Uncu AT, Frary A, Doganlar S. Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing. BMC Genomics 2017; 18:1. [PMID: 28049423 PMCID: PMC5209891 DOI: 10.1186/s12864-016-3406-7] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/09/2016] [Indexed: 11/10/2022] Open
Abstract
Background Solanum pimpinellifolium has high breeding potential for fruit quality traits and has been used as a donor in tomato breeding programs. Unlocking the genetic potential of S. pimpinellifolium requires high-throughput polymorphism identification protocols for QTL mapping and introgression of favourable alleles into cultivated tomato by both positive and background selection. Results In this study we identified SNP loci using a genotyping by sequencing (GBS) approach in an IBL mapping population derived from the cross between a high yielding fresh market tomato and S. pimpinellifolium (LA1589) as the recurrent and donor parents, respectively. A total of 120,983,088 reads were generated by the Illumina HiSeq next-generation sequencing platform. From these reads 448,539 sequence tags were generated. A majority of the sequence tags (84.4%) were uniquely aligned to the tomato genome. A total of 3.125 unique SNP loci were identified as a result of tag alignment to the genome assembly and were used in QTL analysis of 11 fruit quality traits. As a result, 37 QTLs were identified. S. pimpinellifolium contributed favourable alleles for 16 QTLs (43.2%), thus confirming the high breeding potential of this wild species. Conclusions The present work introduced a set of SNPs at sufficiently high density for QTL mapping in populations derived from S. pimpinellifolium (LA1589). Moreover, this study demonstrated the high efficiency of the GBS approach for SNP identification, genotyping and QTL mapping in an interspecific tomato population. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3406-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ibrahim Celik
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Nergiz Gurbuz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Ali Tevfik Uncu
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey.,Pressent Address: Department of Molecular Biology and Genetics, Necmettin Erbakan University, Konya, Turkey
| | - Anne Frary
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey
| | - Sami Doganlar
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, Turkey.
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Salazar JA, Pacheco I, Shinya P, Zapata P, Silva C, Aradhya M, Velasco D, Ruiz D, Martínez-Gómez P, Infante R. Genotyping by Sequencing for SNP-Based Linkage Analysis and Identification of QTLs Linked to Fruit Quality Traits in Japanese Plum ( Prunus salicina Lindl.). FRONTIERS IN PLANT SCIENCE 2017; 8:476. [PMID: 28443103 PMCID: PMC5386982 DOI: 10.3389/fpls.2017.00476] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/20/2017] [Indexed: 05/21/2023]
Abstract
Marker-assisted selection (MAS) in stone fruit (Prunus species) breeding is currently difficult to achieve due to the polygenic nature of the most relevant agronomic traits linked to fruit quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from a reference genome. In this study, GBS was used to genotype 272 seedlings of three F1 Japanese plum (Prunus salicina Lindl) progenies derived from crossing "98-99" (as a common female parent) with "Angeleno," "September King," and "September Queen" as male parents. Raw sequences were aligned to the Peach genome v1, and 42,909 filtered SNPs were obtained after sequence alignment. In addition, 153 seedlings from the "98-99" × "Angeleno" cross were used to develop a genetic map for each parent. A total of 981 SNPs were mapped (479 for "98-99" and 502 for "Angeleno"), covering a genetic distance of 688.8 and 647.03 cM, respectively. Fifty five seedlings from this progeny were phenotyped for different fruit quality traits including ripening time, fruit weight, fruit shape, chlorophyll index, skin color, flesh color, over color, firmness, and soluble solids content in the years 2015 and 2016. Linkage-based QTL analysis allowed the identification of genomic regions significantly associated with ripening time (LG4 of both parents and both phenotyping years), fruit skin color (LG3 and LG4 of both parents and both years), chlorophyll degradation index (LG3 of both parents in 2015) and fruit weight (LG7 of both parents in 2016). These results represent a promising situation for GBS in the identification of SNP variants associated to fruit quality traits, potentially applicable in breeding programs through MAS, in a highly heterozygous crop species such as Japanese plum.
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Affiliation(s)
- Juan A. Salazar
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Igor Pacheco
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de Alimentos, Universidad de ChileSantiago, Chile
| | - Paulina Shinya
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Patricio Zapata
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Claudia Silva
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de Alimentos, Universidad de ChileSantiago, Chile
| | | | | | - David Ruiz
- National Clonal Germplasm Repository, ARS, USDADavis, CA, USA
| | | | - Rodrigo Infante
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
- *Correspondence: Rodrigo Infante
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Zhang Y, Xia X, He Z. The seed dormancy allele TaSdr-A1a associated with pre-harvest sprouting tolerance is mainly present in Chinese wheat landraces. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:81-89. [PMID: 27650191 DOI: 10.1007/s00122-016-2793-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/24/2016] [Indexed: 05/06/2023]
Abstract
We cloned TaSdr - A1 gene, and developed a gene-specific marker for TaSdr - A1 . A QTL for germination index at the TaSdr - A1 locus was identified in the Yangxiaomai/Zhongyou 9507 RIL population. Pre-harvest sprouting (PHS) affects yield and end-use quality in bread wheat (Triticum aestivum L.). In the present study we found an association between the TaSdr-A1 gene and PHS tolerance in bread wheat. TaSdr-A1 on chromosome 2A was cloned using a homologous cloning approach. Sequence analysis of TaSdr-A1 revealed an SNP at position 643, with the G allele being present in genotypes with lower germination index (GI) values and A in those with higher GI. These alleles were designated as TaSdr-A1a and TaSdr-A1b, respectively. A cleaved amplified polymorphism sequence (CAPS) marker Sdr2A based on the SNP was developed, and linkage mapping and QTL analysis were conducted to confirm the association between TaSdr-A1 and seed dormancy. Sdr2A was located in a 2.9 cM interval between SSR markers Xgwm95 and Xgwm372. A QTL for GI at the TaSdr-A1 locus explained 6.6, 7.3, and 8.2 % of the phenotypic variances in a Yangxiaomai/Zhongyou 9507 RIL population grown at Beijing, Shijiazhuang, and the averaged data from the two environments, respectively. Two sets of Chinese wheat cultivars used for validating the TaSdr-A1 polymorphism and the corresponding gene-specific marker Sdr2A showed that TaSdr-A1 was significantly associated with GI. Among 29 accessions with TaSdr-A1a, 24 (82.8 %) were landraces, indicating the importance of Chinese wheat landraces as sources of PHS tolerance. This study identified a novel PHS resistance allele TaSdr-A1a mainly presented in Chinese landraces and it is likely to be the causal gene for QPhs.ccsu-2A.3, providing new information for an understanding of seed dormancy.
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Affiliation(s)
- Yingjun Zhang
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, 162 Hengshan Street, Shijiazhuang, 050035, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
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Zhou Y, Tang H, Cheng MP, Dankwa KO, Chen ZX, Li ZY, Gao S, Liu YX, Jiang QT, Lan XJ, Pu ZE, Wei YM, Zheng YL, Hickey LT, Wang JR. Genome-Wide Association Study for Pre-harvest Sprouting Resistance in a Large Germplasm Collection of Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2017; 8:401. [PMID: 28428791 PMCID: PMC5382224 DOI: 10.3389/fpls.2017.00401] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/09/2017] [Indexed: 05/06/2023]
Abstract
Pre-harvest sprouting (PHS) is mainly caused by the breaking of seed dormancy in high rainfall regions, which leads to huge economic losses in wheat. In this study, we evaluated 717 Chinese wheat landraces for PHS resistance and carried out genome-wide association studies (GWAS) using to 9,740 DArT-seq and 178,803 SNP markers. Landraces were grown across six environments in China and germination testing of harvest-ripe grain was used to calculate the germination rate (GR) for each accession at each site. GR was highly correlated across all environments. A large number of landraces (194) displayed high levels of PHS resistance (i.e., mean GR < 0.20), which included nine white-grained accessions. Overall, white-grained accessions displayed a significantly higher mean GR (42.7-79.6%) compared to red-grained accessions (19.1-56.0%) across the six environments. Landraces from mesic growing zones in southern China showed higher levels of PHS resistance than those sourced from xeric areas in northern and north-western China. Three main quantitative trait loci (QTL) were detected by GWAS: one on 5D that appeared to be novel and two co-located with the grain color transcription factor Tamyb10 on 3A and 3D. An additional 32 grain color related QTL (GCR-QTL) were detected when the set of red-grained landraces were analyzed separately. GCR-QTL occurred at high frequencies in the red-grained accessions and a strong correlation was observed between the number of GCR-QTL and GR (R2 = 0.62). These additional factors could be critical for maintaining high levels of PHS resistance and represent targets for introgression into white-grained wheat cultivars. Further, investigation of the origin of haplotypes associated with the three main QTL revealed that favorable haplotypes for PHS resistance were more common in accessions from higher rainfall zones in China. Thus, a combination of natural and artificial selection likely resulted in landraces incorporating PHS resistance in China.
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Affiliation(s)
- Yong Zhou
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Hao Tang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Meng-Ping Cheng
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Kwame O. Dankwa
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhong-Xu Chen
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhan-Yi Li
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Shang Gao
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Ya-Xi Liu
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Zhi-En Pu
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural UniversityYa’an, China
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, BrisbaneQLD, Australia
| | - Ji-Rui Wang
- Triticeae Research Institute, Sichuan Agricultural UniversityChengdu, China
- *Correspondence: Ji-Rui Wang,
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35
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Nimmakayala P, Abburi VL, Saminathan T, Alaparthi SB, Almeida A, Davenport B, Nadimi M, Davidson J, Tonapi K, Yadav L, Malkaram S, Vajja G, Hankins G, Harris R, Park M, Choi D, Stommel J, Reddy UK. Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L. Sci Rep 2016; 6:38081. [PMID: 27901114 PMCID: PMC5128918 DOI: 10.1038/srep38081] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/03/2016] [Indexed: 12/24/2022] Open
Abstract
Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.
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Affiliation(s)
- Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Venkata L Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Thangasamy Saminathan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Suresh B Alaparthi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Aldo Almeida
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Brittany Davenport
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Marjan Nadimi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Joshua Davidson
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Krittika Tonapi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Lav Yadav
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Sridhar Malkaram
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Gopinath Vajja
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Gerald Hankins
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Robert Harris
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Minkyu Park
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-321, Republic of Korea
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-321, Republic of Korea
| | - John Stommel
- Genetic Improvement of Fruits and Vegetables Laboratory (USDA, ARS), Beltsville, MD-20705, USA
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
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Lin M, Zhang D, Liu S, Zhang G, Yu J, Fritz AK, Bai G. Genome-wide association analysis on pre-harvest sprouting resistance and grain color in U.S. winter wheat. BMC Genomics 2016; 17:794. [PMID: 27729004 PMCID: PMC5059910 DOI: 10.1186/s12864-016-3148-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pre-harvest sprouting (PHS) in wheat can cause substantial reduction in grain yield and end-use quality. Grain color (GC) together with other components affect PHS resistance. Several quantitative trait loci (QTL) have been reported for PHS resistance, and two of them on chromosome 3AS (TaPHS1) and 4A have been cloned. METHODS To determine genetic architecture of PHS and GC and genetic relationships of the two traits, a genome-wide association study (GWAS) was conducted by evaluating a panel of 185 U.S. elite breeding lines and cultivars for sprouting rates of wheat spikes and GC in both greenhouse and field experiments. The panel was genotyped using the wheat 9K and 90K single nucleotide polymorphism (SNP) arrays. RESULTS Four QTL for GC on four chromosomes and 12 QTL for PHS resistance on 10 chromosomes were identified in at least two experiments. QTL for PHS resistance showed varied effects under different environments, and those on chromosomes 3AS, 3AL, 3B, 4AL and 7A were the more frequently identified QTL. The common QTL for GC and PHS resistance were identified on the long arms of the chromosome 3A and 3D. CONCLUSIONS Wheat grain color is regulated by the three known genes on group 3 chromosomes and additional genes from other chromosomes. These grain color genes showed significant effects on PHS resistance in some environments. However, several other QTL that did not affect grain color also played a significant role on PHS resistance. Therefore, it is possible to breed PHS-resistant white wheat by pyramiding these non-color related QTL.
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Affiliation(s)
- Meng Lin
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Dadong Zhang
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Shubing Liu
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Guorong Zhang
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Jianming Yu
- Agronomy Department, Iowa State University Ames, Iowa, 50011, USA
| | - Allan K Fritz
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA
| | - Guihua Bai
- Agronomy Department, Kansas State University, Manhattan, KS, 66506, USA. .,Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA.
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Li R, Erpelding JE. Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing. Genetica 2016; 144:535-545. [PMID: 27604991 DOI: 10.1007/s10709-016-9921-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
The diploid cotton species Gossypium arboreum possesses many favorable agronomic traits such as drought tolerance and disease resistance, which can be utilized in the development of improved upland cotton cultivars. The USDA National Plant Germplasm System maintains more than 1600 G. arboreum accessions. Little information is available on the genetic diversity of the collection thereby limiting the utilization of this cotton species. The genetic diversity and population structure of the G. arboreum germplasm collection were assessed by genotyping-by-sequencing of 375 accessions. Using genome-wide single nucleotide polymorphism sequence data, two major clusters were inferred with 302 accessions in Cluster 1, 64 accessions in Cluster 2, and nine accessions unassigned due to their nearly equal membership to each cluster. These two clusters were further evaluated independently resulting in the identification of two sub-clusters for the 302 Cluster 1 accessions and three sub-clusters for the 64 Cluster 2 accessions. Low to moderate genetic diversity between clusters and sub-clusters were observed indicating a narrow genetic base. Cluster 2 accessions were more genetically diverse and the majority of the accessions in this cluster were landraces. In contrast, Cluster 1 is composed of varieties or breeding lines more recently added to the collection. The majority of the accessions had kinship values ranging from 0.6 to 0.8. Eight pairs of accessions were identified as potential redundancies due to their high kinship relatedness. The genetic diversity and genotype data from this study are essential to enhance germplasm utilization to identify genetically diverse accessions for the detection of quantitative trait loci associated with important traits that would benefit upland cotton improvement.
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Affiliation(s)
- Ruijuan Li
- Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, PO Box 345, Stoneville, MS, 38776, USA
| | - John E Erpelding
- Crop Genetics Research Unit, USDA-ARS, 141 Experiment Station Road, PO Box 345, Stoneville, MS, 38776, USA.
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Bernardo A, Wang S, St. Amand P, Bai G. Using Next Generation Sequencing for Multiplexed Trait-Linked Markers in Wheat. PLoS One 2015; 10:e0143890. [PMID: 26625271 PMCID: PMC4666610 DOI: 10.1371/journal.pone.0143890] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/10/2015] [Indexed: 01/06/2023] Open
Abstract
With the advent of next generation sequencing (NGS) technologies, single nucleotide polymorphisms (SNPs) have become the major type of marker for genotyping in many crops. However, the availability of SNP markers for important traits of bread wheat (Triticum aestivum L.) that can be effectively used in marker-assisted selection (MAS) is still limited and SNP assays for MAS are usually uniplex. A shift from uniplex to multiplex assays will allow the simultaneous analysis of multiple markers and increase MAS efficiency. We designed 33 locus-specific markers from SNP or indel-based marker sequences that linked to 20 different quantitative trait loci (QTL) or genes of agronomic importance in wheat and analyzed the amplicon sequences using an Ion Torrent Proton Sequencer and a custom allele detection pipeline to determine the genotypes of 24 selected germplasm accessions. Among the 33 markers, 27 were successfully multiplexed and 23 had 100% SNP call rates. Results from analysis of "kompetitive allele-specific PCR" (KASP) and sequence tagged site (STS) markers developed from the same loci fully verified the genotype calls of 23 markers. The NGS-based multiplexed assay developed in this study is suitable for rapid and high-throughput screening of SNPs and some indel-based markers in wheat.
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Affiliation(s)
- Amy Bernardo
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Shan Wang
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Paul St. Amand
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
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