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Utebayev MU, Dashkevich SM, Kradetskaya OO, Chilimova IV, Bome NA. Assessment of the genetic diversity of the alleles of gliadin-coding loci in common wheat (Triticum aestivum L.) collections in Kazakhstan and Russia. Vavilovskii Zhurnal Genet Selektsii 2024; 28:263-275. [PMID: 38952702 PMCID: PMC11214902 DOI: 10.18699/vjgb-24-31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 07/03/2024] Open
Abstract
The study of genetic resources using prolamin polymorphism in wheat cultivars from countries with different climatic conditions makes it possible to identify and trace the preference for the selection of the alleles of gliadine-coding loci characteristic of specific conditions. The aim of the study was to determine the "gliadin profile" of the collection of common wheat (Triticum aestivum L.) from breeding centers in Russia and Kazakhstan by studying the genetic diversity of allelic variants of gliadin-coding loci. Intrapopulation (μ ± Sμ) and genetic (H) diversity, the proportion of rare alleles (h ± Sh), identity criterion (I) and genetic similarity (r) of common wheat from eight breeding centers in Russia and Kazakhstan have been calculated. It has been ascertained that the samples of common wheat bred in Kostanay region (Karabalyk Agricultural Experimental Station, Kazakhstan) and Chelyabinsk region (Chelyabinsk Research Institute of Agriculture, Russia) had the highest intrapopulation diversity of gliadin alleles. The proportion of rare alleles (h) at Gli-B1 and Gli-D1 loci was the highest in the wheat cultivars bred by the Federal Center of Agriculture Research of the South-East Region (Saratov region, Russia), which is explained by a high frequency of occurrence of Gli-B1e (86 %) and Gli-D1a (89.9 %) alleles. Based on identity criterion (I), the studied samples of common wheat from different regions of Kazakhstan and Russia have differences in gliadin-coding loci. The highest value of I = 619.0 was found when comparing wheat samples originated from Kostanay and Saratov regions, and the lowest I = 114.4, for wheat cultivars from Tyumen and Chelyabinsk regions. Some region-specific gliadin alleles in wheat samples have been identified. A combination of Gli-A1f, Gli-B1e and Gli-Da alleles has been identified in the majority of wheat samples from Kazakhstan and Russia. Alleles (Gli-A1f, Gli-A1i, Gli-A1m, Gli-A1o, Gli-B1e, Gli-D1a, Gli-D1f, Gli-A2q, Gli-B2o, and Gli-D2a) turned out to be characteristic and were found with varying frequency in wheat cultivars in eight regions of Russia and Kazakhstan. The highest intravarietal polymorphism (51.1 %) was observed in wheat cultivars bred in Omsk region (Russia) and the lowest (16.6 %), in Pavlodar region (Kazakhstan). On the basis of the allele frequencies, a "gliadin profile" of wheat from various regions and breeding institutions of Russia and Kazakhstan was compiled, which can be used for the selection of parent pairs in the breeding process, the control of cultivars during reproduction, as well as for assessing varietal purity.
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Affiliation(s)
- M U Utebayev
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy-1, Akmola Region, Kazakhstan
| | - S M Dashkevich
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy-1, Akmola Region, Kazakhstan
| | - O O Kradetskaya
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy-1, Akmola Region, Kazakhstan
| | - I V Chilimova
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy-1, Akmola Region, Kazakhstan
| | - N A Bome
- University of Tyumen, Tyumen, Russia
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Tam NT, Nhan DK. Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice ( Oryza sativa L.). BIOLOGY 2024; 13:358. [PMID: 38785840 PMCID: PMC11117668 DOI: 10.3390/biology13050358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.
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Affiliation(s)
- Nguyen Thanh Tam
- Mekong Delta Development Research Institute, Can Tho University, Campus 2, 3-2 Street, Can Tho 94115, Vietnam
| | - Dang Kieu Nhan
- Mekong Delta Development Research Institute, Can Tho University, Campus 2, 3-2 Street, Can Tho 94115, Vietnam
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Khassanova G, Oshergina I, Ten E, Jatayev S, Zhanbyrshina N, Gabdola A, Gupta NK, Schramm C, Pupulin A, Philp-Dutton L, Anderson P, Sweetman C, Jenkins CL, Soole KL, Shavrukov Y. Zinc finger knuckle genes are associated with tolerance to drought and dehydration in chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1354413. [PMID: 38766473 PMCID: PMC11099236 DOI: 10.3389/fpls.2024.1354413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/17/2024] [Indexed: 05/22/2024]
Abstract
Chickpea (Cicer arietinum L.) is a very important food legume and needs improved drought tolerance for higher seed production in dry environments. The aim of this study was to determine diversity and genetic polymorphism in zinc finger knuckle genes with CCHC domains and their functional analysis for practical improvement of chickpea breeding. Two CaZF-CCHC genes, Ca04468 and Ca07571, were identified as potentially important candidates associated with plant responses to drought and dehydration. To study these genes, various methods were used including Sanger sequencing, DArT (Diversity array technology) and molecular markers for plant genotyping, gene expression analysis using RT-qPCR, and associations with seed-related traits in chickpea plants grown in field trials. These genes were studied for genetic polymorphism among a set of chickpea accessions, and one SNP was selected for further study from four identified SNPs between the promoter regions of each of the two genes. Molecular markers were developed for the SNP and verified using the ASQ and CAPS methods. Genotyping of parents and selected breeding lines from two hybrid populations, and SNP positions on chromosomes with haplotype identification, were confirmed using DArT microarray analysis. Differential expression profiles were identified in the parents and the hybrid populations under gradual drought and rapid dehydration. The SNP-based genotypes were differentially associated with seed weight per plant but not with 100 seed weight. The two developed and verified SNP molecular markers for both genes, Ca04468 and Ca07571, respectively, could be used for marker-assisted selection in novel chickpea cultivars with improved tolerance to drought and dehydration.
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Affiliation(s)
- Gulmira Khassanova
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Irina Oshergina
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Evgeniy Ten
- Department of Crop Breeding, A.I.Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Nursaule Zhanbyrshina
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Ademi Gabdola
- Faculty of Agronomy, S.Seifullin Kazakh AgroTechnical Research University, Astana, Kazakhstan
| | - Narendra K. Gupta
- Department of Plant Physiology, Sri Karan Narendra (SNK) Agricultural University, Jobster, Rajastan, India
| | - Carly Schramm
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Antonio Pupulin
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Lauren Philp-Dutton
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Peter Anderson
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Crystal Sweetman
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Colin L.D. Jenkins
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering (Biological Sciences), Flinders University, Adelaide, SA, Australia
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Hussain S, Habib M, Ahmed Z, Sadia B, Bernardo A, Amand PS, Bai G, Ghori N, Khan AI, Awan FS, Maqbool R. Genotyping-by-Sequencing Based Molecular Genetic Diversity of Pakistani Bread Wheat ( Triticum aestivum L.) Accessions. Front Genet 2022; 13:772517. [PMID: 35464861 PMCID: PMC9019749 DOI: 10.3389/fgene.2022.772517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022] Open
Abstract
Spring wheat (Triticum aestivum L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ∼40% world population. Genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.
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Affiliation(s)
- Shabbir Hussain
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Madiha Habib
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Zaheer Ahmed
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Bushra Sadia
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Amy Bernardo
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Paul St Amand
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Guihua Bai
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Nida Ghori
- USDA, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, United States
| | - Azeem I Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Faisal S Awan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Rizwana Maqbool
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
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Mekbib Y, Tesfaye K, Dong X, Saina JK, Hu GW, Wang QF. Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern. BMC PLANT BIOLOGY 2022; 22:69. [PMID: 35164709 PMCID: PMC8842891 DOI: 10.1186/s12870-022-03449-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 06/04/2023]
Abstract
BACKGROUND Coffea arabica L. is an economically important agricultural crop and the most popular beverage worldwide. As a perennial crop with recalcitrant seed, conservation of the genetic resources of coffee can be achieved through the complementary approach of in-situ and ex-situ field genebank. In Ethiopia, a large collection of C. arabica L. germplasm is preserved in field gene banks. Here, we report the whole-genome resequencing of 90 accessions from Choche germplasm bank representing garden and forest-based coffee production systems using Illumina sequencing technology. RESULTS The genome sequencing generated 6.41 billion paired-end reads, with a mean of 71.19 million reads per sample. More than 93% of the clean reads were mapped onto the C. arabica L. reference genome. A total of 11.08 million variants were identified, among which 9.74 million (87.9%) were SNPs (Single nucleotide polymorphisms) and 1.34 million (12.1%) were InDels. In all accessions, genomic variants were unevenly distributed across the coffee genome. The phylogenetic analysis using the SNP markers displayed distinct groups. CONCLUSIONS Resequencing of the coffee accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs discovered in this study might contribute to the variation in important pathways of genes for important agronomic traits such as caffeine content, yield, disease, and pest in coffee. Moreover, the genome resequencing data and the genetic markers identified from 90 accessions provide insight into the genetic variation of the coffee germplasm and facilitate a broad range of genetic studies.
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Affiliation(s)
- Yeshitila Mekbib
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Josphat K Saina
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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Maung TZ, Chu SH, Park YJ. Functional Haplotypes and Evolutionary Insight into the Granule-Bound Starch Synthase II ( GBSSII) Gene in Korean Rice Accessions (KRICE_CORE). Foods 2021; 10:2359. [PMID: 34681408 PMCID: PMC8535093 DOI: 10.3390/foods10102359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022] Open
Abstract
Granule-bound starch synthase 2 (GBSSII), a paralogous isoform of GBSSI, carries out amylose biosynthesis in rice. Unlike GBSSI, it mainly functions in transient organs, such as leaves. Despite many reports on the starch gene family, little is known about the genetics and genomics of GBSSII. Haplotype analysis was conducted to unveil genetic variations (SNPs and InDels) of GBSSII (OS07G0412100) and it was also performed to gain evolutionary insight through genetic diversity, population genetic structure, and phylogenetic analyses using the KRICE_CORE set (475 rice accessions). Thirty nonsynonymous SNPs (nsSNPs) were detected across the diverse GBSSII coding regions, representing 38 haplotypes, including 13 cultivated, 21 wild, and 4 mixed (a combination of cultivated and wild) varieties. The cultivated haplotypes (C_1-C_13) contained more nsSNPs across the GBSSII genomic region than the wild varieties. Nucleotide diversity analysis highlighted the higher diversity values of the cultivated varieties (weedy = 0.0102, landrace = 0.0093, and bred = 0.0066) than the wild group (0.0045). The cultivated varieties exhibited no reduction in diversity during domestication. Diversity reduction in the japonica and the wild groups was evidenced by the negative Tajima's D values under purifying selection, suggesting the domestication signatures of GBSSII; however, balancing selection was indicated by positive Tajima's D values in indica. Principal component analysis and population genetics analyses estimated the ambiguous evolutionary relationships among the cultivated and wild rice groups, indicating highly diverse structural features of the rice accessions within the GBSSII genomic region. FST analysis differentiated most of the classified populations in a range of greater FST values. Our findings provide evolutionary insights into GBSSII and, consequently, a molecular breeding program can be implemented for select desired traits using these diverse nonsynonymous (functional) alleles.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea;
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea;
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Tomar V, Dhillon GS, Singh D, Singh RP, Poland J, Joshi AK, Tiwari BS, Kumar U. Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat ( Triticum aestivum L .). PeerJ 2021; 9:e11593. [PMID: 34221720 PMCID: PMC8231316 DOI: 10.7717/peerj.11593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
Abstract
Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon's information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.
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Affiliation(s)
- Vipin Tomar
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gandhinagar, Gujarat, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India
| | - Guriqbal Singh Dhillon
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Daljit Singh
- The Climate Corporation, Bayer Crop Science, Creve Coeur, MO, USA
| | - Ravi Prakash Singh
- Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India.,Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
| | - Budhi Sagar Tiwari
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gandhinagar, Gujarat, India
| | - Uttam Kumar
- Borlaug Institute for South Asia, New Delhi, Delhi, India.,International Maize and Wheat Improvement Centre, New Delhi, Delhi, India.,Global Wheat Program, International Maize and Wheat Improvement Centre, Texcoco, Mexico
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Zotova L, Shamambaeva N, Lethola K, Alharthi B, Vavilova V, Smolenskaya SE, Goncharov NP, Kurishbayev A, Jatayev S, Gupta NK, Gupta S, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y. TaDrAp1 and TaDrAp2, Partner Genes of a Transcription Repressor, Coordinate Plant Development and Drought Tolerance in Spelt and Bread Wheat. Int J Mol Sci 2020; 21:E8296. [PMID: 33167455 PMCID: PMC7663959 DOI: 10.3390/ijms21218296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/10/2023] Open
Abstract
Down-regulator associated protein, DrAp1, acts as a negative cofactor (NC2α) in a transcription repressor complex together with another subunit, down-regulator Dr1 (NC2β). In binding to promotors and regulating the initiation of transcription of various genes, DrAp1 plays a key role in plant transition to flowering and ultimately in seed production. TaDrAp1 and TaDrAp2 genes were identified, and their expression and genetic polymorphism were studied using bioinformatics, qPCR analyses, a 40K Single nucleotide polymorphism (SNP) microarray, and Amplifluor-like SNP genotyping in cultivars of bread wheat (Triticum aestivum L.) and breeding lines developed from a cross between spelt (T. spelta L.) and bread wheat. TaDrAp1 was highly expressed under non-stressed conditions, and at flowering, TaDrAp1 expression was negatively correlated with yield capacity. TaDrAp2 showed a consistently low level of mRNA production. Drought caused changes in the expression of both TaDrAp1 and TaDrAp2 genes in opposite directions, effectively increasing expression in lower yielding cultivars. The microarray 40K SNP assay and Amplifluor-like SNP marker, revealed clear scores and allele discriminations for TaDrAp1 and TaDrAp2 and TaRht-B1 genes. Alleles of two particular homeologs, TaDrAp1-B4 and TaDrAp2-B1, co-segregated with grain yield in nine selected breeding lines. This indicated an important regulatory role for both TaDrAp1 and TaDrAp2 genes in plant growth, ontogenesis, and drought tolerance in bread and spelt wheat.
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Affiliation(s)
- Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan 010000, Kazakhstan; (L.Z.); (N.S.); (A.K.)
| | - Nasgul Shamambaeva
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan 010000, Kazakhstan; (L.Z.); (N.S.); (A.K.)
| | - Katso Lethola
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Badr Alharthi
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Valeriya Vavilova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (V.V.); (S.E.S.); (N.P.G.)
| | - Svetlana E. Smolenskaya
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (V.V.); (S.E.S.); (N.P.G.)
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (V.V.); (S.E.S.); (N.P.G.)
| | - Akhylbek Kurishbayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan 010000, Kazakhstan; (L.Z.); (N.S.); (A.K.)
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan 010000, Kazakhstan; (L.Z.); (N.S.); (A.K.)
| | - Narendra K. Gupta
- Department of Plant Physiology, SKN Agriculture University, Jobner 303329, Rajasthan, India; (N.K.G.); (S.G.)
| | - Sunita Gupta
- Department of Plant Physiology, SKN Agriculture University, Jobner 303329, Rajasthan, India; (N.K.G.); (S.G.)
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Peter A. Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA 5042, Australia; (K.L.); (B.A.); (C.S.); (P.A.A.); (C.L.D.J.); (K.L.S.)
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Yang X, Tan B, Liu H, Zhu W, Xu L, Wang Y, Fan X, Sha L, Zhang H, Zeng J, Wu D, Jiang Y, Hu X, Chen G, Zhou Y, Kang H. Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing. Front Genet 2020; 11:580782. [PMID: 33101397 PMCID: PMC7545058 DOI: 10.3389/fgene.2020.580782] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Obtaining information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N. In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content was in the range of 0.1 to 0.4, with a mean of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was slightly higher as indicated by the observed heterozygosity (H o) = 0.23, and unbiased diversity index (uh) = 0.34. The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.
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Affiliation(s)
- Xiu Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Binwen Tan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haijiao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lili Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xigui Hu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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10
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Rasheed A, Takumi S, Hassan MA, Imtiaz M, Ali M, Morgunov AI, Mahmood T, He Z. Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1503-1520. [PMID: 31897516 DOI: 10.1007/s00122-019-03523-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.
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Affiliation(s)
- Awais Rasheed
- 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), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe, 657-8501, Japan
| | - Muhammad Adeel Hassan
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Mohsin Ali
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Alex I Morgunov
- International Maize and Wheat Improvement Center (CIMMYT), Yenimahalle, Ankara, 06170, Turkey
| | - Tariq Mahmood
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - 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), CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
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11
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Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties. Int J Genomics 2019; 2019:4168045. [PMID: 31687375 PMCID: PMC6811786 DOI: 10.1155/2019/4168045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/01/2019] [Accepted: 08/19/2019] [Indexed: 01/30/2023] Open
Abstract
Recently, rice breeding program has shown increased interests on the pigmented rice varieties due to their benefits to human health. However, the genetic variation of pigmented rice varieties is still scarce and remains unexplored. Hence, we performed genome-wide SNP analysis from the genome resequencing of four Malaysian pigmented rice varieties, representing two black and two red rice varieties. The genome of four pigmented varieties was mapped against Nipponbare reference genome sequences, and 1.9 million SNPs were discovered. Of these, 622 SNPs with polymorphic sites were identified in 258 protein-coding genes related to metabolism, stress response, and transporter. Comparative analysis of 622 SNPs with polymorphic sites against six rice SNP datasets from the Ensembl Plants variation database was performed, and 70 SNPs were identified as novel SNPs. Analysis of SNPs in the flavonoid biosynthetic genes revealed 40 nonsynonymous SNPs, which has potential as molecular markers for rice seed colour identification. The highlighted SNPs in this study show effort in producing valuable genomic resources for application in the rice breeding program, towards the genetic improvement of new and improved pigmented rice varieties.
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12
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Bahri BA, Daverdin G, Xu X, Cheng JF, Barry KW, Brummer EC, Devos KM. Natural variation in genes potentially involved in plant architecture and adaptation in switchgrass (Panicum virgatum L.). BMC Evol Biol 2018; 18:91. [PMID: 29898656 PMCID: PMC6000970 DOI: 10.1186/s12862-018-1193-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 05/15/2018] [Indexed: 11/24/2022] Open
Abstract
Background Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4× = 36) perennial C4 grass (Poaceae family) native to North America and a feedstock crop for cellulosic biofuel production, has a large potential for genetic improvement due to its high genotypic and phenotypic variation. In this study, we analyzed single nucleotide polymorphism (SNP) variation in 372 switchgrass genotypes belonging to 36 accessions for 12 genes putatively involved in biomass production to investigate signatures of selection that could have led to ecotype differentiation and to population adaptation to geographic zones. Results A total of 11,682 SNPs were mined from ~ 15 Gb of sequence data, out of which 251 SNPs were retained after filtering. Population structure analysis largely grouped upland accessions into one subpopulation and lowland accessions into two additional subpopulations. The most frequent SNPs were in homozygous state within accessions. Sixty percent of the exonic SNPs were non-synonymous and, of these, 45% led to non-conservative amino acid changes. The non-conservative SNPs were largely in linkage disequilibrium with one haplotype being predominantly present in upland accessions while the other haplotype was commonly present in lowland accessions. Tajima’s test of neutrality indicated that PHYB, a gene involved in photoperiod response, was under positive selection in the switchgrass population. PHYB carried a SNP leading to a non-conservative amino acid change in the PAS domain, a region that acts as a sensor for light and oxygen in signal transduction. Conclusions Several non-conservative SNPs in genes potentially involved in plant architecture and adaptation have been identified and led to population structure and genetic differentiation of ecotypes in switchgrass. We suggest here that PHYB is a key gene involved in switchgrass natural selection. Further analyses are needed to determine whether any of the non-conservative SNPs identified play a role in the differential adaptation of upland and lowland switchgrass. Electronic supplementary material The online version of this article (10.1186/s12862-018-1193-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA. .,Laboratory of Bioaggressors and Integrated Protection in Agriculture, The National Agronomic Institute of Tunisia, University of Carthage, 43 Avenue Charles-Nicolle, 1082, Tunis, Tunisia.
| | - Guillaume Daverdin
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Present address: Vinson Edward Ltd, Faversham, ME13 8UP, UK
| | - Xiangyang Xu
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.,Present address: USDA-ARS, Wheat, Peanut and Other Field Crops Research Unit, Stillwater, OK, 74075, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, CA, 94598, USA
| | - Kerrie W Barry
- DOE Joint Genome Institute, Walnut Creek, California, CA, 94598, USA
| | - E Charles Brummer
- Plant Breeding Center, Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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Alipour H, Bihamta MR, Mohammadi V, Peyghambari SA, Bai G, Zhang G. Genotyping-by-Sequencing (GBS) Revealed Molecular Genetic Diversity of Iranian Wheat Landraces and Cultivars. FRONTIERS IN PLANT SCIENCE 2017; 8:1293. [PMID: 28912785 PMCID: PMC5583605 DOI: 10.3389/fpls.2017.01293] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/07/2017] [Indexed: 05/22/2023]
Abstract
Background: Genetic diversity is an essential resource for breeders to improve new cultivars with desirable characteristics. Recently, genotyping-by-sequencing (GBS), a next-generation sequencing (NGS) technology that can simplify complex genomes, has now be used as a high-throughput and cost-effective molecular tool for routine breeding and screening in many crop species, including the species with a large genome. Results: We genotyped a diversity panel of 369 Iranian hexaploid wheat accessions including 270 landraces collected between 1931 and 1968 in different climate zones and 99 cultivars released between 1942 to 2014 using 16,506 GBS-based single nucleotide polymorphism (GBS-SNP) markers. The B genome had the highest number of mapped SNPs while the D genome had the lowest on both the Chinese Spring and W7984 references. Structure and cluster analyses divided the panel into three groups with two landrace groups and one cultivar group, suggesting a high differentiation between landraces and cultivars and between landraces. The cultivar group can be further divided into four subgroups with one subgroup was mostly derived from Iranian ancestor(s). Similarly, landrace groups can be further divided based on years of collection and climate zones where the accessions were collected. Molecular analysis of variance indicated that the genetic variation was larger between groups than within group. Conclusion: Obvious genetic diversity in Iranian wheat was revealed by analysis of GBS-SNPs and thus breeders can select genetically distant parents for crossing in breeding. The diverse Iranian landraces provide rich genetic sources of tolerance to biotic and abiotic stresses, and they can be useful resources for the improvement of wheat production in Iran and other countries.
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Affiliation(s)
- Hadi Alipour
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia UniversityUrmia, Iran
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of TehranKaraj, Iran
- Agronomy Department, Kansas State University, ManhattanKS, United States
| | - Mohammad R. Bihamta
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of TehranKaraj, Iran
| | - Valiollah Mohammadi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of TehranKaraj, Iran
| | - Seyed A. Peyghambari
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of TehranKaraj, Iran
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture – Agricultural Research Service, ManhattanKS, United States
| | - Guorong Zhang
- Agronomy Department, Kansas State University, ManhattanKS, United States
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14
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Chen K, Zhou YX, Li K, Qi LX, Zhang QF, Wang MC, Xiao JH. A novel three-round multiplex PCR for SNP genotyping with next generation sequencing. Anal Bioanal Chem 2016; 408:4371-7. [PMID: 27113460 DOI: 10.1007/s00216-016-9536-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/27/2016] [Accepted: 03/31/2016] [Indexed: 11/28/2022]
Abstract
Owing to the high throughput and low cost, next generation sequencing has attracted much attention for SNP genotyping application for researchers. Here, we introduce a new method based on three-round multiplex PCR to precisely genotype SNPs with next generation sequencing. This method can as much as possible consume the equivalent amount of each pair of specific primers to largely eliminate the amplification discrepancy between different loci. After the PCR amplification, the products can be directly subjected to next generation sequencing platform. We simultaneously amplified 37 SNP loci of 757 samples and sequenced all amplicons on ion torrent PGM platform; 90.5 % of the target SNP loci were accurately genotyped (at least 15×) and 90.4 % amplicons had uniform coverage with a variation less than 50-fold. Ligase detection reaction (LDR) was performed to genotype the 19 SNP loci (as part of the 37 SNP loci) with 91 samples randomly selected from the 757 samples, and 99.5 % genotyping data were consistent with the next generation sequencing results. Our results demonstrate that three-round PCR coupled with next generation sequencing is an efficient and economical genotyping approach. Graphical Abstract The schematic diagram of three-round PCR.
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Affiliation(s)
- Ke Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 05003365, China
| | - Yu-Xun Zhou
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Kai Li
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Li-Xin Qi
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Qi-Fei Zhang
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Mao-Chun Wang
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Jun-Hua Xiao
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China.
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Shavrukov Y. Comparison of SNP and CAPS markers application in genetic research in wheat and barley. BMC PLANT BIOLOGY 2016; 16 Suppl 1:11. [PMID: 26821936 PMCID: PMC4895257 DOI: 10.1186/s12870-015-0689-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
BACKGROUND Barley and bread wheat show large differences in frequencies of Single Nucleotide Polymorphism (SNP) as determined from genome-wide studies. These frequencies have been estimated as 2.4-3 times higher in the entire barley genome than within each diploid genomes of wheat (A, B or D). However, barley SNPs within individual genes occur significantly more frequently than quoted. Differences between wheat and barley are based on the origin and evolutionary history of the species. Bread wheat contains rarer SNPs due to the double genetic 'bottle-neck' created by natural hybridisation and spontaneous polyploidisation. Furthermore, wheat has the lowest level of useful SNP-derived markers while barley is estimated to have the highest level of polymorphism. RESULTS Different strategies are required for the development of suitable molecular markers in these cereal species. For example, SNP markers based on high-throughput technology (Infinium or KASP) are very effective and useful in both barley and bread wheat. In contrast, Cleaved Amplified Polymorphic Sequences (CAPS) are more widely and successfully employed in small-scale experiments with highly polymorphic genetic regions containing multiple SNPs in barley, but not in wheat. However, preliminary 'in silico' search databases for assessing the potential value of SNPs have yet to be developed. CONCLUSIONS This mini-review summarises results supporting the development of different strategies for the application of effective SNP and CAPS markers in wheat and barley.
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Affiliation(s)
- Yuri Shavrukov
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia.
- Department of Biological Sciences, Flinders University, Adelaide, Australia.
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