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Sabouri H, Pezeshkian Z, Taliei F, Akbari M, Kazerani B. Detection of closely linked QTLs and candidate genes controlling germination indices in response to drought and salinity stresses in barley. Sci Rep 2024; 14:15656. [PMID: 38977885 PMCID: PMC11231201 DOI: 10.1038/s41598-024-66452-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
The aim of current study was to identify closely linked QTLs and candidate genes related to germination indices under control, salinity and drought conditions in barley. A total of nine (a major), 28 (eight major) and 34 (five major) closely linked QTLs were mapped on the seven chromosomes in response to control, drought and salinity conditions using genome-wide composite interval mapping, respectively. The major QTLs can be used in marker-assisted selection (MAS) projects to increase tolerance to drought and salinity stresses during the germination. Overall, 422 unique candidate genes were associated with most major QTLs. Moreover, gene ontology analysis showed that candidate genes mostly involved in biological process related to signal transduction and response to stimulus in the pathway of resistance to drought and salinity stresses. Also, the protein-protein interaction network was identified 10 genes. Furthermore, 10 genes were associated with receptor-like kinase family. In addition, 16 transcription factors were detected. Three transcription factors including B3, bHLH, and FAR1 had the most encoding genes. Totally, 60 microRNAs were traced to regulate the target genes. Finally, the key genes are a suitable and reliable source for future studies to improve resistance to abiotic stress during the germination of barley.
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Affiliation(s)
- Hossein Sabouri
- Department of Plant Production, College of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad, Iran.
| | - Zahra Pezeshkian
- Department of Animal Sciences, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
- BioGenTAC Inc., Technology Incubator of Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, Iran
| | - Fakhtak Taliei
- Department of Plant Production, College of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad, Iran
| | - Mahjoubeh Akbari
- Department of Plant Production, College of Agriculture Science and Natural Resource, Gonbad Kavous University, Gonbad, Iran
| | - Borzo Kazerani
- Department of Plant Breeding and Biotechnology, Faculty of Plant Production, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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Hassett K, Muria-Gonzalez MJ, Martin A, Karakaya A, Çelik Oğuz A, Bakonyi J, Knight NL, Prins R, Ellwood SR. Global Spread, Genetic Differentiation, and Selection of Barley Spot Form Net Blotch Isolates. PHYTOPATHOLOGY 2024; 114:1542-1553. [PMID: 38619562 DOI: 10.1094/phyto-11-23-0442-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Spot form net blotch, caused by Pyrenophora teres f. maculata, is a significant necrotrophic disease of barley that spread worldwide in the twentieth century. Genetic relationships were analyzed to determine the diversity, survival, and dispersal of a diverse collection of 346 isolates from Australia, Southern Africa, North America, Asia Minor, and Europe. The results, based on genome-wide DArTseq data, indicated that isolates from Turkey were the most differentiated with regional sub-structuring, together with individuals closely related to geographically distant genotypes. Elsewhere, population subdivision related to country of origin was evident, although low levels of admixturing was found that may represent rare genotypes or migration from unsampled populations. Canadian isolates were the next most diverged, and Australian and South African the most closely related. With the exception of Turkish isolates, multiple independent Cyp51A mutation events (which confer insensitivity to demethylation inhibitor fungicides) between countries and within regions was evident, with strong selection for a transposable element insertion at the 3' end of the promoter and counterselection elsewhere. Individuals from Western Australia shared genomic regions and Cyp51A haplotypes with South African isolates, suggesting a recent common origin. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Kealan Hassett
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Mariano Jordi Muria-Gonzalez
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Aziz Karakaya
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Dışkapı, Ankara 06110, Turkey
| | - Arzu Çelik Oğuz
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Dışkapı, Ankara 06110, Turkey
| | - Jószef Bakonyi
- Plant Protection Institute, HUN-REN Centre for Agricultural Research, Herman Ottó str. 15, 1022 Budapest, Hungary
| | - Noel L Knight
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Renée Prins
- CenGen (Pty) Ltd., Worcester, 6850, South Africa
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
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Liu M, Zhang Y, Shaw RK, Zhang X, Li J, Li L, Li S, Adnan M, Jiang F, Bi Y, Yin X, Fan X. Genome-Wide Association Study and Prediction of Tassel Weight of Tropical Maize Germplasm in Multi-Parent Population. Int J Mol Sci 2024; 25:1756. [PMID: 38339032 PMCID: PMC10855296 DOI: 10.3390/ijms25031756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Tassel weight (TW) is a crucial agronomic trait that significantly affects pollen supply and grain yield development in maize breeding. To improve maize yield and develop new varieties, a comprehensive understanding of the genetic mechanisms underlying tassel weight is essential. In this study, tropical maize inbred lines, namely CML312, CML373, CML444, and YML46, were selected as female parents and crossed with the elite maize inbred line Ye107, which served as the common male parent, to develop a multi-parent population comprising four F8 recombinant inbred line (RIL) subpopulations. Using 6616 high-quality single nucleotide polymorphism (SNP) markers, we conducted genome-wide association analysis (GWAS) and genomic selection (GS) on 642 F8 RILs in four subpopulations across three different environments. Through GWAS, we identified 16 SNPs that were significantly associated with TW, encompassing two stable loci expressed across multiple environments. Furthermore, within the candidate regions of these SNPs, we discovered four novel candidate genes related to TW, namely Zm00001d044362, Zm00001d011048, Zm00001d011049, and Zm00001d031173 distributed on chromosomes 1, 3, and 8, which have not been previously reported. These genes are involved in processes such as signal transduction, growth and development, protein splicing, and pollen development, all of which play crucial roles in inflorescence meristem development, directly affecting TW. The co-localized SNP, S8_137379725, on chromosome 8 was situated within a 16.569 kb long terminal repeat retrotransposon (LTR-RT), located 22.819 kb upstream and 26.428 kb downstream of the candidate genes (Zm00001d011048 and Zm00001d011049). When comparing three distinct GS models, the BayesB model demonstrated the highest accuracy in predicting TW. This study establishes the theoretical foundation for future research into the genetic mechanisms underlying maize TW and the efficient breeding of high-yielding varieties with desired tassel weight through GS.
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Affiliation(s)
- Meichen Liu
- School of Agriculture, Yunnan University, Kunming 650500, China; (M.L.); (X.Z.); (J.L.); (L.L.); (S.L.)
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (M.A.); (F.J.); (Y.B.); (X.Y.)
| | - Ranjan K. Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (M.A.); (F.J.); (Y.B.); (X.Y.)
| | - Xingjie Zhang
- School of Agriculture, Yunnan University, Kunming 650500, China; (M.L.); (X.Z.); (J.L.); (L.L.); (S.L.)
| | - Jinfeng Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (M.L.); (X.Z.); (J.L.); (L.L.); (S.L.)
| | - Linzhuo Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (M.L.); (X.Z.); (J.L.); (L.L.); (S.L.)
| | - Shaoxiong Li
- School of Agriculture, Yunnan University, Kunming 650500, China; (M.L.); (X.Z.); (J.L.); (L.L.); (S.L.)
| | - Muhammad Adnan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (M.A.); (F.J.); (Y.B.); (X.Y.)
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (M.A.); (F.J.); (Y.B.); (X.Y.)
| | - Yaqi Bi
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (M.A.); (F.J.); (Y.B.); (X.Y.)
| | - Xingfu Yin
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (M.A.); (F.J.); (Y.B.); (X.Y.)
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (Y.Z.); (R.K.S.); (M.A.); (F.J.); (Y.B.); (X.Y.)
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Srivastava A, Pusuluri M, Balakrishnan D, Vattikuti JL, Neelamraju S, Sundaram RM, Mangrauthia SK, Ram T. Identification and Functional Characterization of Two Major Loci Associated with Resistance against Brown Planthoppers ( Nilaparvata lugens (Stål)) Derived from Oryza nivara. Genes (Basel) 2023; 14:2066. [PMID: 38003009 PMCID: PMC10671472 DOI: 10.3390/genes14112066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
The brown planthopper (BPH) is a highly destructive pest of rice, causing significant economic losses in various regions of South and Southeast Asia. Researchers have made promising strides in developing resistance against BPH in rice. Introgression line RPBio4918-230S, derived from Oryza nivara, has shown consistent resistance to BPH at both the seedling and adult stages of rice plants. Segregation analysis has revealed that this resistance is governed by two recessive loci, known as bph39(t) and bph40(t), contributing to 21% and 22% of the phenotypic variance, respectively. We later mapped the genes using a backcross population derived from a cross between Swarna and RPBio4918-230S. We identified specific marker loci, namely RM8213, RM5953, and R4M17, on chromosome 4, flanking the bph39(t) and bph40(t) loci. Furthermore, quantitative expression analysis of candidate genes situated between the RM8213 and R4M17 markers was conducted. It was observed that eight genes exhibited up-regulation in RPBio4918-230S and down-regulation in Swarna after BPH infestation. One gene of particular interest, a serine/threonine-protein kinase receptor (STPKR), showed significant up-regulation in RPBio4918-230S. In-depth sequencing of the susceptible and resistant alleles of STPKR from Swarna and RPBio4918-230S, respectively, revealed numerous single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) mutations, both in the coding and regulatory regions of the gene. Notably, six of these mutations resulted in amino acid substitutions in the coding region of STPKR (R5K, I38L, S120N, T319A, T320S, and F348S) when compared to Swarna and the reference sequence of Nipponbare. Further validation of these mutations in a set of highly resistant and susceptible backcross inbred lines confirmed the candidacy of the STPKR gene with respect to BPH resistance controlled by bph39(t) and bph40(t). Functional markers specific for STPKR have been developed and validated and can be used for accelerated transfer of the resistant locus to elite rice cultivars.
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Affiliation(s)
- Akanksha Srivastava
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | - Madhu Pusuluri
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Divya Balakrishnan
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | - Jhansi Lakshmi Vattikuti
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | - Sarla Neelamraju
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | - Raman Meenakshi Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | | | - Tilathoo Ram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
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Maanju S, Jasrotia P, Yadav SS, Kashyap PL, Kumar S, Jat MK, Lal C, Sharma P, Singh G, Singh GP. Deciphering the genetic diversity and population structure of wild barley germplasm against corn leaf aphid, Rhopalosiphum maidis (Fitch). Sci Rep 2023; 13:17313. [PMID: 37828115 PMCID: PMC10570286 DOI: 10.1038/s41598-023-42717-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
Corn-leaf aphid (CLA-Rhopalosiphum maidis) is a major insect pest of barley (Hordeum vulgare) causing yield loss upto 30% under severe infestation. Keeping in view of the availability of very few sources of CLA resistance in barley, the present investigation was framed to assess the genetic diversity and population structure of 43 wild barley (H. vulgare subsp. spontaneum) genotypes using eight microsatellite markers against R. maidis. Three statistical methods viz. multivariate-hierarchical clustering, Bayesian clustering and PCoA, unanimously grouped genotypes into three subpopulations (K = 3) with 25.58% (SubPop1-Red), 39.53% (SubPop2-Green) and 34.88% (SubPop3-Blue) genotypes including admixtures. Based on Q ≥ 66.66%, 37.20% genotypes formed a superficial "Mixed/Admixture" subpopulation. All polymorphic SSR markers generated 36 alleles, averaging to 4.5 alleles/locus (2-7 range). The PIC and H were highest in MS31 and lowest in MS28, with averages of 0.66 and 0.71. MAF and mean genetic diversity were 0.16 and 89.28%, respectively. All these parameters indicated the presence of predominant genetic diversity and population structure amongst the studied genotypes. Based on AII, only 6 genotypes were found to be R. maidis resistant. SubPop3 had 91.66% (11) of the resistant or moderately resistant genotypes. SubPop3 also had the most pure genotypes (11), the least aphid infestation (8.78), and the highest GS (0.88), indicating its suitability for future R. maidis resistance breeding initiatives.
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Affiliation(s)
- Sunny Maanju
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
- CCS Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Poonam Jasrotia
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India.
| | | | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Manoj Kumar Jat
- CCS Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Chuni Lal
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Preeti Sharma
- CCS Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
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Alzoheiry AM, Ghumaiz NSA, Motawei MI, Kassem MA. Water productivity and growth parameters of Fawn-tall fescue and Tekapo-orchard grass under deficit irrigation in arid zones. BRAZ J BIOL 2023; 84:e272544. [PMID: 37222377 DOI: 10.1590/1519-6984.272544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/04/2023] [Indexed: 05/25/2023] Open
Abstract
This study aimed to determine the drought stress response of Fawn-tall fescue and Tekapo-orchard grass and investigate a drought stress resistance marker. Grass genotypes were grown under four Irrigation treatments I1 equivalent to 0.3 standard crop evapotranspiration (ETc), I2 equivalent to 0.65 ETc, I3 equivalent to 0.75 ETc, and I4 equivalent to 1.2 ETc. Plant height, fresh weight, dry weight were measured and the Water productivity (WP) were calculated. The results showed a reduction in the growth of both grass genotypes as the drought stress increased as indicated by the shorter plants and reduction in fresh and dry weight. However, the WP results showed that the Fawn-tall fescue endured the drought stress better than the Tekapo-orchard grass as indicated by the constant values of the plant WP across the tested irrigation treatments. The results was confirmed by the amplification of dehydrin genes where Fawn-tall fescue was found to be homozygous for dehydrin genes.
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Affiliation(s)
- A M Alzoheiry
- Qassim University, College of Agriculture and Veterinary Medicine, Department of Plant Production and Protection, Burydah, Saudi Arabia
- Damanhur University, Faculty of Agriculture, Department of Natural Resources and Agricultural Engineering, Damanhur, Egypt
| | - N S Al Ghumaiz
- Qassim University, College of Agriculture and Veterinary Medicine, Department of Plant Production and Protection, Burydah, Saudi Arabia
| | - M I Motawei
- Qassim University, College of Agriculture and Veterinary Medicine, Department of Plant Production and Protection, Burydah, Saudi Arabia
- Alexandria University, College of Agriculture, Department of Crop Science, Alexandria, Egypt
| | - M A Kassem
- Cairo University, Faculty of Agriculture, Department of Agricultural Engineering, Giza, Egypt
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Wang Y, Bi Y, Jiang F, Shaw RK, Sun J, Hu C, Guo R, Fan X. Mapping and Functional Analysis of QTL for Kernel Number per Row in Tropical and Temperate-Tropical Introgression Lines of Maize ( Zea mays L.). Curr Issues Mol Biol 2023; 45:4416-4430. [PMID: 37232750 DOI: 10.3390/cimb45050281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F7 recombinant inbred line (RIL) populations were created using a temperate-tropical introgression line TML418 and a tropical inbred line CML312 as female parents and a backbone maize inbred line Ye107 as the common male parent. Bi-parental quantitative trait locus (QTL) mapping and genome-wide association analysis (GWAS) were then performed on 399 lines of the two maize RIL populations for KNR in two different environments using 4118 validated single nucleotide polymorphism (SNP) markers. This study aimed to: (1) detect molecular markers and/or the genomic regions associated with KNR; (2) identify the candidate genes controlling KNR; and (3) analyze whether the candidate genes are useful in improving GY. The authors reported a total of 7 QTLs tightly linked to KNR through bi-parental QTL mapping and identified 21 SNPs significantly associated with KNR through GWAS. Among these, a highly confident locus qKNR7-1 was detected at two locations, Dehong and Baoshan, with both mapping approaches. At this locus, three novel candidate genes (Zm00001d022202, Zm00001d022168, Zm00001d022169) were identified to be associated with KNR. These candidate genes were primarily involved in the processes related to compound metabolism, biosynthesis, protein modification, degradation, and denaturation, all of which were related to the inflorescence development affecting KNR. These three candidate genes were not reported previously and are considered new candidate genes for KNR. The progeny of the hybrid Ye107 × TML418 exhibited strong heterosis for KNR, which the authors believe might be related to qKNR7-1. This study provides a theoretical foundation for future research on the genetic mechanism underlying KNR in maize and the use of heterotic patterns to develop high-yielding hybrids.
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Affiliation(s)
- Yuling Wang
- Institute of Resource Plants, Yunnan University, Kunming 650504, China
| | - Yaqi Bi
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Ranjan Kumar Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jiachen Sun
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650500, China
| | - Can Hu
- Institute of Resource Plants, Yunnan University, Kunming 650504, China
| | - Ruijia Guo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
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Sabouri H, Alegh SM, Sahranavard N, Sanchouli S. SSR Linkage Maps and Identification of QTL Controlling Morpho-Phenological Traits in Two Iranian Wheat RIL Populations. BIOTECH 2022; 11:biotech11030032. [PMID: 35997340 PMCID: PMC9397039 DOI: 10.3390/biotech11030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 11/22/2022] Open
Abstract
Wheat is one of the essential grains grown in large areas. Identifying the genetic structure of agronomic and morphological traits of wheat can help to discover the genetic mechanisms of grain yield. In order to map the morpho-phenological traits, an experiment was conducted in the two cropping years of 2020 and 2021 on the university farm of the Faculty of Agriculture, GonbadKavous University. This study used two F8 populations, including 120 lines resulting from Gonbad × Zagros and Gonbad × Kuhdasht. The number of days to physiological maturity, number of days to flowering, number of germinated grains, number of tillers, number of tillers per plant, grain filling periods, plant height, peduncle length, spike length, awn length, spike weight, peduncle diameter, flag leaf length and weight, number of spikelets per spike, number of grains per spike, grain length, grain width, 1000-grain weight, biomass, grain yield, harvest index, straw-weight, and number of fertile spikelets per spike were measured. A total of 21 and 13 QTLs were identified for 11 and 13 traits in 2020 and 2021, respectively. In 2020, qGL-3D and qHI-1A were identified for grain length and harvest index on chromosomes 3D and 1A, explaining over 20% phenotypic variation, respectively. qNT-5B, qNTS-2D, and qSL-1D were identified on chromosomes 5B, 2D, and 1D with the LOD scores of 4.5, 4.13, and 3.89 in 2021, respectively.
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Affiliation(s)
- Hossein Sabouri
- Department of Plant Production, College of Agricultural Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
- Correspondence: (H.S.); (S.S.); Tel.: +98-911-143-8917 (H.S.); +98-911-793-0631 (S.S.)
| | - Sharifeh Mohammad Alegh
- Department of Plant Production, College of Agricultural Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
| | - Narges Sahranavard
- Department of Biology, College of Science, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
| | - Somayyeh Sanchouli
- Department of Plant Production, College of Agricultural Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
- Correspondence: (H.S.); (S.S.); Tel.: +98-911-143-8917 (H.S.); +98-911-793-0631 (S.S.)
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Makhtoum S, Sabouri H, Gholizadeh A, Ahangar L, Katouzi M. QTLs Controlling Physiological and Morphological Traits of Barley (Hordeum vulgare L.) Seedlings under Salinity, Drought, and Normal Conditions. BIOTECH 2022; 11:biotech11030026. [PMID: 35892931 PMCID: PMC9326576 DOI: 10.3390/biotech11030026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
To identify the genomic regions for the physiological and morphological traits of barley genotypes under normal salinity and drought, a set of 103 recombinant inbred line (RIL) populations, developed between Badia and Kavir crosses, was evaluated under phytotron conditions in a completely randomized design in 2019. Linkage maps were prepared using 152 SSR markers, 72 ISSR, 7 IRAP, 29 CAAT, 27 SCoT, and 15 iPBS alleles. The markers were assigned to seven barley chromosomes and covered 999.29 centimorgans (cM) of the barley genome. In addition, composite interval mapping showed 8, 9, and 26 quantitative trait loci (QTLs) under normal, drought, and salinity stress conditions, respectively. Our results indicate the importance of chromosomes 1, 4, 5, and 7 in salinity stress. These regions were involved in genes controlling stomata length (LR), leaf number (LN), leaf weight (LW), and genetic score (SCR). Three major stable pleiotropic QTLs (i.e., qSCS-1, qRLS-1, and qLNN-1) were associated with SCR, root length (RL), and root number (RN) in both treatments (i.e., normal and salinity), and two major stable pleiotropic QTLs (i.e., qSNN-3 and qLWS-3) associated with the stomata number (SN) and LW appeared to be promising for marker-assisted selection (MAS). Two major-effect QTLs (i.e., SCot8-B-CAAT5-D and HVM54-Bmag0571) on chromosomes 1 and 2 were characterized for their positive allele effect, which can be used to develop barley varieties concerning drought conditions. The new alleles (i.e., qLWS-4a, qSLS-4, qLNS-7b, qSCS-7, and qLNS-7a) identified in this study are useful in pyramiding elite alleles for molecular breeding and marker assisted selection for improving salinity tolerance in barley.
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Affiliation(s)
- Somayyeh Makhtoum
- Department of Plant Production, Faculty of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad 4971799151, Iran; (S.M.); (A.G.); (L.A.)
| | - Hossein Sabouri
- Department of Plant Production, Faculty of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad 4971799151, Iran; (S.M.); (A.G.); (L.A.)
- Correspondence: or (H.S.); (M.K.); Tel.: +98-91-1143-8917 (H.S.); +41-77-9660486 (M.K.)
| | - Abdollatif Gholizadeh
- Department of Plant Production, Faculty of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad 4971799151, Iran; (S.M.); (A.G.); (L.A.)
| | - Leila Ahangar
- Department of Plant Production, Faculty of Agriculture Science and Natural Resources, Gonbad Kavous University, Gonbad 4971799151, Iran; (S.M.); (A.G.); (L.A.)
| | - Mahnaz Katouzi
- Crop Génome Dynamics Group, Agroscope Changins, 1260 Nyon, Switzerland
- Correspondence: or (H.S.); (M.K.); Tel.: +98-91-1143-8917 (H.S.); +41-77-9660486 (M.K.)
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10
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Raouf HB, Sabouri A, Allahgholipour M. Study of Physicochemical Properties of Rice Grains, Association and Haplotype Analysis Using SSR Genetic Markers. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422060060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Shamsabadi EE, Sabouri H, Soughi H, Sajadi SJ. Using of Molecular Markers in Prediction of Wheat (Triticum aestivum L.) Hybrid Grain Yield Based on Artificial Intelligence Methods and Multivariate Statistics. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542205009x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Genetic diversity, population structure and relationship of Ethiopian barley (Hordeum vulgare L.) landraces as revealed by SSR markers. J Genet 2022. [DOI: 10.1007/s12041-021-01346-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Zhang Q, Li Y, Li Y, Fahima T, Shen Q, Xie C. Introgression of the Powdery Mildew Resistance Genes Pm60 and Pm60b from Triticum urartu to Common Wheat Using Durum as a 'Bridge'. Pathogens 2021; 11:pathogens11010025. [PMID: 35055973 PMCID: PMC8778237 DOI: 10.3390/pathogens11010025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/20/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022] Open
Abstract
Powdery mildew, caused by the fungus Blumeria graminis f. sp. tritici (Bgt), has limited wheat yields in many major wheat-production areas across the world. Introducing resistance genes from wild relatives into cultivated wheat can enrich the genetic resources for disease resistance breeding. The powdery mildew resistance gene Pm60 was first identified in diploid wild wheat Triticum urartu (T. urartu). In this study, we used durum as a ‘bridge’ approach to transfer Pm60 and Pm60b into hexaploid common wheat. Synthetic hexaploid wheat (SHW, AABBAuAu), developed by crossing T. urartu (AuAu) with durum (AABB), was used for crossing and backcrossing with common wheat. The Pm60 alleles were tracked by molecular markers and the resistance to powdery mildew. From BC1F1 backcross populations, eight recombinant types were identified based on five Pm60-flanking markers, which indicated different sizes of the introgressed chromosome segments from T. urartu. Moreover, we have selected two resistance-harboring introgression lines with high self-fertility, which could be easily used in wheat breeding system. Our results showed that the durum was an excellent ‘bridge’ for introducing the target gene from diploid T. urartu into the hexaploid cultivated wheat. Moreover, these introgression lines could be deployed in wheat resistance breeding programs, together with the assistance of the molecular markers for Pm60 alleles.
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Affiliation(s)
- Qiang Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Yinghui Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel;
- Correspondence: (Y.L.); (Q.S.); (C.X.); Tel.: +86-010-62731064 (Q.S.)
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel;
| | - Qianhua Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.L.); (Q.S.); (C.X.); Tel.: +86-010-62731064 (Q.S.)
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
- Correspondence: (Y.L.); (Q.S.); (C.X.); Tel.: +86-010-62731064 (Q.S.)
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Ghomi K, Rabiei B, Sabouri H, Gholamalipour Alamdari E. Association analysis, genetic diversity and population structure of barley (Hordeum vulgare L.) under heat stress conditions using SSR and ISSR markers linked to primary and secondary metabolites. Mol Biol Rep 2021; 48:6673-6694. [PMID: 34495461 DOI: 10.1007/s11033-021-06652-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Barley is one of the major cereal crops, which can provide a significant source of genes for stress tolerance due to its high diversity and adaptability. Metabolite traits are considered to be significant for adaptation of barley to heat stress. METHODS AND RESULTS In the present study, genetic relationships between 120 barley genotypes were determined with 50 simple sequence repeat (SSR) and 26 inter simple sequence repeat (ISSR) markers under heat stress and non-stress conditions. Moreover, genetic diversity of barley accessions was investigated using the studied markers covering 7 chromosomes of barley. RESULTS In general, 153 and 85 polymorphic alleles were detected for SSR and ISSR and number of the observed polymorphic allele varied between 2-9 and 2-6, with an average of 3.26 and 3.26 alleles per locus, respectively. Markers of Bmag0223, GBMS180/180, HVM7, ISSR22, ISSR25, and ISSR48 were the most informative due to their high polymorphism information content value demonstrating that putative techniques utilized in this research can be powerful and valuable tools in breeding program of barley. Association analysis was performed between 9 important traits and SSR and ISSR markers using four statistical models. The results revealed that the model containing both population structure (Q) and general similarity in genetic background arising from shared kinship (K) factors reduced false positive associations between markers and phenotypes. CONCLUSIONS According to the results, some of markers related to more than one trait under normal conditions (ISSR31-2, HVM62, and GBMS180/180) and heat stress conditions (ISSR20-5, EBmac635, HVM14, and ISSR37-3) were determined, which can be considered to be the most interesting candidates for further studies and simultaneously will provide a useful target for the future breeding programs, such as marker-assisted selection (MAS).
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Affiliation(s)
- Khadijeh Ghomi
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Persian Gulf Highway, P.O. Box: 41635-1314, Rasht, Guilan, Iran
| | - Babak Rabiei
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Persian Gulf Highway, P.O. Box: 41635-1314, Rasht, Guilan, Iran.
| | - Hossein Sabouri
- Department of Plant Production, Faculty of Agriculture and Natural Resources, Gonbad University, Shahid Fallahi Street, Gonbad-e Kāvūs, Golestan, Iran
| | - Ebrahim Gholamalipour Alamdari
- Department of Plant Production, Faculty of Agriculture and Natural Resources, Gonbad University, Shahid Fallahi Street, Gonbad-e Kāvūs, Golestan, Iran
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15
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Zhang Q, Wei W, Zuansun X, Zhang S, Wang C, Liu N, Qiu L, Wang W, Guo W, Ma J, Peng H, Hu Z, Sun Q, Xie C. Fine Mapping of the Leaf Rust Resistance Gene Lr65 in Spelt Wheat 'Altgold'. FRONTIERS IN PLANT SCIENCE 2021; 12:666921. [PMID: 34262578 PMCID: PMC8274547 DOI: 10.3389/fpls.2021.666921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Wheat leaf rust (also known as brown rust), caused by the fungal pathogen Puccinia triticina Erikss. (Pt), is one by far the most troublesome wheat disease worldwide. The exploitation of resistance genes has long been considered as the most effective and sustainable method to control leaf rust in wheat production. Previously the leaf rust resistance gene Lr65 has been mapped to the distal end of chromosome arm 2AS linked to molecular marker Xbarc212. In this study, Lr65 was delimited to a 0.8 cM interval between flanking markers Alt-64 and AltID-11, by employing two larger segregating populations obtained from crosses of the resistant parent Altgold Rotkorn (ARK) with the susceptible parents Xuezao and Chinese Spring (CS), respectively. 24 individuals from 622 F2 plants of crosses between ARK and CS were obtained that showed the recombination between Lr65 gene and the flanking markers Alt-64 and AltID-11. With the aid of the CS reference genome sequence (IWGSC RefSeq v1.0), one SSR marker was developed between the interval matched to the Lr65-flanking marker and a high-resolution genetic linkage map was constructed. The Lr65 was finally located to a region corresponding to 60.11 Kb of the CS reference genome. The high-resolution genetic linkage map founded a solid foundation for the map-based cloning of Lr65 and the co-segregating marker will facilitate the marker-assisted selection (MAS) of the target gene.
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16
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Salter WT, Li S, Dracatos PM, Barbour MM. Identification of quantitative trait loci for dynamic and steady-state photosynthetic traits in a barley mapping population. AOB PLANTS 2020; 12:plaa063. [PMID: 33408849 PMCID: PMC7759950 DOI: 10.1093/aobpla/plaa063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/18/2020] [Indexed: 05/29/2023]
Abstract
Enhancing the photosynthetic induction response to fluctuating light has been suggested as a key target for improvement in crop breeding programmes, with the potential to substantially increase whole-canopy carbon assimilation and contribute to crop yield potential. Rubisco activation may be the main physiological process that will allow us to achieve such a goal. In this study, we assessed the phenotype of Rubisco activation rate in a doubled haploid (DH) barley mapping population [131 lines from a Yerong/Franklin (Y/F) cross] after a switch from moderate to saturating light. Rates of Rubisco activation were found to be highly variable across the mapping population, with a median activation rate of 0.1 min-1 in the slowest genotype and 0.74 min-1 in the fastest genotype. A unique quantitative trait locus (QTL) for Rubisco activation rate was identified on chromosome 7H. This is the first report on the identification of a QTL for Rubisco activation rate in planta and the discovery opens the door to marker-assisted breeding to improve whole-canopy photosynthesis of barley. This also suggests that genetic factors other than the previously characterized Rubisco activase (RCA) isoforms on chromosome 4H control Rubisco activity. Further strength is given to this finding as this QTL co-localized with QTLs identified for steady-state photosynthesis and stomatal conductance. Several other distinct QTLs were identified for these steady-state traits, with a common overlapping QTL on chromosome 2H, and distinct QTLs for photosynthesis and stomatal conductance identified on chromosomes 4H and 5H, respectively. Future work should aim to validate these QTLs under field conditions so that they can be used to aid plant breeding efforts.
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Affiliation(s)
- William T Salter
- School of Life and Environmental Sciences, Sydney Institute of Agriculture, The University of Sydney, Brownlow Hill, NSW, Australia
| | - Si Li
- School of Life and Environmental Sciences, Sydney Institute of Agriculture, The University of Sydney, Brownlow Hill, NSW, Australia
| | - Peter M Dracatos
- Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Margaret M Barbour
- School of Life and Environmental Sciences, Sydney Institute of Agriculture, The University of Sydney, Brownlow Hill, NSW, Australia
- School of Science, University of Waikato, Hillcrest, Hamilton, New Zealand
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17
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Mohammadi SA, Abdollahi Sisi N, Sadeghzadeh B. The influence of breeding history, origin and growth type on population structure of barley as revealed by SSR markers. Sci Rep 2020; 10:19165. [PMID: 33154389 PMCID: PMC7645596 DOI: 10.1038/s41598-020-75339-4] [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: 07/29/2019] [Accepted: 10/13/2020] [Indexed: 11/08/2022] Open
Abstract
Natural and mass selection during domestication and cultivation favored particular traits of interest in barley. In the present study, population structure, and genetic relationships among 144 accessions of barley landraces and breeding materials from various countries were studied using a set of 77 and 72 EST-SSR and gSSR markers, respectively distributed on seven chromosomes of barley. In total, 262 and 429 alleles were amplified in 77 EST-SSRs and 72 gSSR loci, respectively. Out of which, 185 private/group-specific alleles were identified in the landraces compared with 14 in "cultivar and advanced breeding lines", indicating the possibility to introgress favorite alleles from landraces into breeding materials. Comparative analysis of genetic variation among breeding materials, Iranian landraces, and exotic landraces revealed higher genetic diversity in Iranian landraces compared with others. A total of 37, 15, and 14 private/group-specific alleles were identified in Iranian landraces, exotic landraces, and breeding materials, respectively. The most likely groups for 144 barley genotypes were three as inferred using model- and distance-based clustering as well as principal coordinate analysis which assigned the landraces and breeding materials into separate groups. The distribution of alleles was found to be correlated with population structure, domestication history and eco-geographical factors. The high allelic richness in the studied set of barley genotype provides insights into the available diversity and allows the construction of core groups based on maximizing allelic diversity for use in barley breeding programs.
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Affiliation(s)
- Seyyed Abolghasem Mohammadi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, 51666, Tabriz, Iran.
- Center of Excellence in Cereal Molecular Breeding, University of Tabriz, 51666, Tabriz, Iran.
- Center for Cell Pathology, Department of Life Sciences, Khazar University, Baku, AZ1096, Azerbaijan.
| | - Nayyer Abdollahi Sisi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, 51666, Tabriz, Iran
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18
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Tolmay VL, Sydenham SL, Sikhakhane TN, Nhlapho BN, Tsilo TJ. Elusive Diagnostic Markers for Russian Wheat Aphid Resistance in Bread Wheat: Deliberating and Reviewing the Status Quo. Int J Mol Sci 2020; 21:ijms21218271. [PMID: 33158282 PMCID: PMC7663459 DOI: 10.3390/ijms21218271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Russian wheat aphid, Diuraphis noxia (Kurdjumov), is a severe pest of wheat, Triticum aestivum L., throughout the world. Resistant cultivars are viewed as the most economical and environmentally viable control available. Studies to identify molecular markers to facilitate resistance breeding started in the 1990s, and still continue. This paper reviews and discusses the literature pertaining to the D. noxia R-genes on chromosome 7D, and markers reported to be associated with them. Individual plants with known phenotypes from a panel of South African wheat accessions are used as examples. Despite significant inputs from various research groups over many years, diagnostic markers for resistance to D. noxia remain elusive. Factors that may have impeded critical investigation, thus blurring the accumulation of a coherent body of information applicable to Dn resistance, are discussed. This review calls for a more fastidious approach to the interpretation of results, especially considering the growing evidence pointing to the complex regulation of aphid resistance response pathways in plants. Appropriate reflection on prior studies, together with emerging knowledge regarding the complexity and specificity of the D. noxia–wheat resistance interaction, should enable scientists to address the challenges of protecting wheat against this pest in future.
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Affiliation(s)
- Vicki L. Tolmay
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
- Department of Life and Consumer Sciences, University of South Africa, Pretoria 0002, South Africa
- Correspondence:
| | - Scott L. Sydenham
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
| | - Thandeka N. Sikhakhane
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
- Department of Life and Consumer Sciences, University of South Africa, Pretoria 0002, South Africa
| | - Bongiwe N. Nhlapho
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
| | - Toi J. Tsilo
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
- Department of Life and Consumer Sciences, University of South Africa, Pretoria 0002, South Africa
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Agarwal P, Balyan HS, Gupta PK. Identification of modifiers of the plant height in wheat using an induced dwarf mutant controlled by RhtB4c allele. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2283-2289. [PMID: 33268929 PMCID: PMC7688886 DOI: 10.1007/s12298-020-00904-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/29/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
In wheat, 25 Rht genes for dwarfness are known, which include both, GA-insensitive and GA-responsive genes. The GA-insensitive Rht genes have been widely used, although, their suitability under abiotic stress conditions has been questioned. This necessitated a search for alternative GA-responsive, spontaneous and induced dwarfing genes. We earlier reported an induced dwarf mutant ('dwarf mutant-3'; 44 cm), and the mutant allele was named Rht4c allele (2BL). This dwarf mutant was not suitable for cultivation due to its extra dwarf nature. Therefore, we searched for naturally occurring QTLs, which would modify the phenotype of 'dwarf-mutant-3' using 'mutant-assisted gene identification and characterization' (MAGIC) approach. For this purpose, the 'dwarf mutant-3' was crossed with a tall wheat cv. NP114 and homozygous mutant F2 plants (~ 25% of the progeny) were selected, which were phenotyped for plant height and genotyped using SSR markers. The data were utilized for QTL analysis and plant height. Six modifier QTLs were identified on chromosomes 2A, 2B and 4A. Two QTLs each on 2A and 2B were responsible for increase in plant height (described as 'enhancer modifiers'), whereas the remaining two QTLs located on 4A were responsible for reducing the plant height (described as 'suppressor modifiers'). It was hypothesized that the enhancer QTLs could be exploited for the development of semi-dwarf high yielding genotypes containing Rht4c allele. This is the first study of its kind in wheat demontsrating that the MAGIC approach could be used for identification of modifiers of the mutant phenotypes of other traits for wheat improvement.
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Affiliation(s)
- Priyanka Agarwal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - H. S. Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
| | - P. K. Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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Rossarolla MD, Tomazetti TC, Vieira LN, Guerra MP, Klabunde GHF, Scherer RF, Pescador R, Nodari RO. Identification and characterization of SSR markers of Guadua chacoensis (Rojas) Londoño & P.M. Peterson and transferability to other bamboo species. 3 Biotech 2020; 10:273. [PMID: 32523867 DOI: 10.1007/s13205-020-02268-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022] Open
Abstract
The aim of this study was to develop simple sequence repeat (SSR) markers for genetic studies on G. chacoensis, as well as to evaluate their transferability to other bamboo species. Genomic DNA was isolated from G. chacoensis and its partial sequencing was used to find SSR loci. The obtained sequencing data were de novo assembled using the software CLC Genomics Workbench® 8.0v. The SSR loci primers were identified and designed with the software SSRLocator. The selected markers were validated using 56 plants sampled in seven populations from southern Brazil. The markers with potential polymorphism were selected and fluorescently labeled for characterization by capillary electrophoresis. In total, 92 SSR loci were found in G. chacoensis contigs. Suitable primers were designed for 70 SSR loci, and the remaining 22 SSR loci did not have sequences for primer development. Out of 35 selected SSR markers, after PCR optimization, 10 with high polymorphism potential were characterized. These loci can be used in genetic analyses of G. chacoensis and all of them were successfully transferred to other bamboo species. Non-polymorphic loci require further tests with additional plants, from different populations, to identify possibilities of their use.
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Affiliation(s)
- Márcia D Rossarolla
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
| | - Tiago C Tomazetti
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
| | - Leila N Vieira
- Programa de Pós-Graduação em Botânica, Universidade Federal do Paraná, Av. Cel. Francisco H. dos Santos, 100, Curitiba, Paraná 81531-980 Brazil
| | - Miguel P Guerra
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
- Programa de Pós-graduação em Ecossistemas Agrícolas e Naturais, Universidade Federal de Santa Catarina, Campus Curitibanos, Rodovia Ulysses Gaboardi 3000, Curitibanos, Santa Catarina 89520-000 Brazil
| | - Gustavo H F Klabunde
- Estação Experimental de Itajaí, Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina, Rodovia Antônio Heil, n°6800, Itajaí, Santa Catarina 88318-112 Brazil
| | - Ramon F Scherer
- Estação Experimental de Itajaí, Empresa de Pesquisa Agropecuária e Extensão Rural de Santa Catarina, Rodovia Antônio Heil, n°6800, Itajaí, Santa Catarina 88318-112 Brazil
| | - Rosete Pescador
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
| | - Rubens O Nodari
- Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga,1346, Florianópolis, Santa Catarina 88040-900 Brazil
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21
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Discovery and characterisation of a new leaf rust resistance gene introgressed in wheat from wild wheat Aegilops peregrina. Sci Rep 2020; 10:7573. [PMID: 32371881 PMCID: PMC7200655 DOI: 10.1038/s41598-020-64166-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/08/2020] [Indexed: 12/03/2022] Open
Abstract
Wild wheat species Aegilops peregrina (UpUpSpSp), harbours resistance to various diseases including leaf rust and stripe rust. Inheritance studies in a recombinant inbred line population of wheat-Ae. peregrina introgression line IL pau16061 revealed the transfer of a single major dominant gene conditioning all stage resistance, herein temporarily designated as LrAp. Genomic in situ hybridisation of IL pau16061, resistant and susceptible RILs with U- and S-genome DNA probes confirmed that the introgression with leaf rust resistance is from the Up genome of Ae. peregrina. Fluorescence in situ hybridisation using chromosome specific probes identified Up genome introgression to be on the long arm of wheat chromosome 6B. To genetically map LrAp, bulked segregant analysis was combined with resistance gene enrichment sequencing (MapRenSeq). Five nucleotide binding leucine-rich repeat contigs distinguished resistant and susceptible bulks and single nucleotide polymorphism (SNP) markers from these contigs co-segregated with LrAp. All five RenSeq NB_ARC contigs showed identity with the long arm of wheat chromosome 6B confirming the introgression on 6BL which we propose is a compensating translocation from Ae. peregrina chromosome 6UpL due to homoeology between the alien and wheat chromosomes. The SNP markers developed in this study will aid in cloning and marker assisted gene pyramiding of LrAp.
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Akanksha S, Lakshmi VJ, Singh AK, Deepthi Y, Chirutkar PM, Ramdeen, Balakrishnan D, Sarla N, Mangrauthia SK, Ram T. Genetics of novel brown planthopper Nilaparvata lugens (Stål) resistance genes in derived introgression lines from the interspecific cross O. sativa var. Swarna × O. nivara. J Genet 2019. [DOI: 10.1007/s12041-019-1158-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Akanksha S, Jhansi Lakshmi V, Singh AK, Deepthi Y, Chirutkar PM, Balakrishnan D, Sarla N, Mangrauthia SK, Ram T. Genetics of novel brown planthopper Nilaparvata lugens (Stål) resistance genes in derived introgression lines from the interspecific cross O. sativa var. Swarna × O. nivara. J Genet 2019; 98:113. [PMID: 31819024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The brown planthopper (BPH) Nilaparvata lugens (Stål) (Homoptera: Delphacidae) is considered a threat to rice (Oryza sativa ssp.) crop in many parts of the world including India. Among the BPH-resistance (R) genes so far reported in rice, most of them are ineffective against BPH biotype 4 predominant in the Indian sub-continent. In this study, we show the introgression line RPBio4918-230S was identified as BPH resistant after five years of rigorous screening at seedling stage and two years at tillering and reproductive stages. The inheritance of resistance indicated that two recessive genes are involved at seedling and reproductive stages. The allelic relation with known genes using linked reported markers suggested that the genes present in RPBio4918-230S are different. We report here the genetics of the two newly introgressed BPH resistance genes from O. nivara in the background of Swarna which are effective at all the important growth stages. The genes have been tentatively named as bph39(t) and bph40(t). The honeydew area (feeding rate) and days to wilt parameters observed at 30 days after sowing in BC1F3 indicated that newly introgressed genes have both antibiosis and tolerance mechanisms for resistance. The BPH resistance genes identified in this study would facilitate the breeding of broad spectrum and durable resistance in rice against BPH biotype 4.
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Affiliation(s)
- S Akanksha
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500 030, India.
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Zhang X, Zhang L, Schinnerl J, Sun WB, Chen G. Genetic diversity and population structure of Hibiscus aridicola, an endangered ornamental species in dry-hot valleys of Jinsha River. PLANT DIVERSITY 2019; 41:300-306. [PMID: 31934674 PMCID: PMC6951272 DOI: 10.1016/j.pld.2019.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
Hibiscus aridicola is an endangered ornamental shrub of the family Malvaceae that is endemic to the dry-hot valleys of Jinsha River in southwestern China. This species is a typical plant species with extremely small populations (PSESP). To support and monitor future conservation, develop management measures, and genotype this species, we performed extensive field studies together with genetic analyses. Specifically, we screened eleven microsatellite loci of 69 individuals of H. aridicola from four accessions. The population genetics analyses indicated that H. aridicola possesses high genetic diversity at both the population (0.6962-0.7293) and species level (0.7837) compared to other endemic/endangered species in China. The low differentiation of populations (Fst = 0.0971) and the high gene flow between populations of H. aridicola (Nm = 2.3236) could be due to its distribution along rivers in the hot-valleys of the Jinsha River and the wind-mediated dispersal of its seeds. Furthermore, the genetic diversity of H. aridicola is slightly positively correlated with geographic distance. Two populations are undergoing a genetic bottleneck, and require more specific attention from conservationists. Additionally, our analyses of the population genetics of H. aridicola demonstrate that the declines in populations are not the result of the internal genetics of these populations but due to external human activities over the past decades.
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Affiliation(s)
- Xin Zhang
- Yunnan Forestry Technological College, Kunming, 650224, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming, 650204, China
| | - Le Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming, 650204, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Johann Schinnerl
- Chemodiversity Research Group, Division of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, A-1030, Vienna, Austria
| | - Wei-Bang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming, 650204, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Gao Chen
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming, 650204, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
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Pandey AK, Madhu P, Bhat BV. Down-Regulation of CYP79A1 Gene Through Antisense Approach Reduced the Cyanogenic Glycoside Dhurrin in [ Sorghum bicolor (L.) Moench] to Improve Fodder Quality. Front Nutr 2019; 6:122. [PMID: 31544105 PMCID: PMC6729101 DOI: 10.3389/fnut.2019.00122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/24/2019] [Indexed: 11/13/2022] Open
Abstract
A major limitation for the utilization of sorghum forage is the production of the cyanogenic glycoside dhurrin in its leaves and stem that may cause the death of cattle feeding on it at the pre-flowering stage. Therefore, we attempted to develop transgenic sorghum plants with reduced levels of hydrogen cyanide (HCN) by antisense mediated down-regulation of the expression of cytochrome P450 CYP79A1, the key enzyme of the dhurrin biosynthesis pathway. CYP79A1 cDNA was isolated and cloned in antisense orientation, driven by rice Act1 promoter. Shoot meristem explants of sorghum cultivar CSV 15 were transformed by the particle bombardment method and 27 transgenics showing the integration of transgene were developed. The biochemical assay for HCN in the transgenic sorghum plants confirmed significantly reduced HCN levels in transgenic plants and their progenies. The HCN content in the transgenics varied from 5.1 to 149.8 μg/g compared to 192.08 μg/g in the non-transformed control on dry weight basis. Progenies with reduced HCN content were advanced after each generation till T3. In T3 generation, progenies of two promising events were tested which produced highly reduced levels of HCN (mean of 62.9 and 76.2 μg/g, against the control mean of 221.4 μg/g). The reduction in the HCN levels of transgenics confirmed the usefulness of this approach for reducing HCN levels in forage sorghum plants. The study effectively demonstrated that the antisense CYP79A1 gene deployment was effective in producing sorghum plants with lower HCN content which are safer for cattle to feed on.
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Affiliation(s)
- Arun K. Pandey
- ICAR-Indian Institute of Millets Research (IIMR), Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pusuluri Madhu
- ICAR-Indian Institute of Millets Research (IIMR), Hyderabad, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Narang D, Kaur S, Steuernagel B, Ghosh S, Dhillon R, Bansal M, Uauy C, Wulff BBH, Chhuneja P. Fine mapping of Aegilops peregrina co-segregating leaf and stripe rust resistance genes to distal-most end of 5DS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1473-1485. [PMID: 30706082 DOI: 10.1007/s00122-019-03293-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Novel rust resistance genes LrP and YrP from Ae. peregrina identified on chromosome 5D and the linked markers will aid deployment of these genes in combination with other major/minor genes. Aegilops peregrina, a wild tetraploid relative of wheat with genome constitution UUSS, displays genetic variation for resistance to leaf and stripe (yellow) rust. The wheat Ae. peregrina introgression line, IL pau16058, harbouring leaf and stripe rust resistance, was crossed with wheat cv. WL711 to generate an F2:3 mapping population. Inheritance studies on this population indicated the transfer of dominant co-segregating resistance to leaf and stripe rust. Ethyl methane sulphonate mutagenesis of IL pau16058 identified independent loss-of-function mutants for leaf and stripe rust resistance, indicating that the leaf and stripe rust resistance is controlled by independent genes, herein designated LrP and YrP, respectively. A high-resolution genetic map of LrP and YrP was constructed using the Illumina Infinium iSelect 90K wheat array and resistance gene enrichment sequencing (RenSeq) markers. The map spans 4.19 cM on the distal-most region of the short arm of chromosome 5D, consisting of eight SNP markers and one microsatellite marker. LrP and YrP co-segregated with markers BS00163889 and 5DS44573_snp and was flanked distally by the SNP marker BS00129707 and proximally by 5DS149010, defining a 15.71 Mb region in the RefSeq v1.0 genome assembly.
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Affiliation(s)
- Deepika Narang
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Roopan Dhillon
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Mitaly Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
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Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Okporie E, Onyishi G, Utobo E, Ekwu L, Swaray S, Jalloh M. Marker-assisted selection and gene pyramiding for resistance to bacterial leaf blight disease of rice (Oryza sativa L.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1584054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Yussuf Oladosu
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emmanuel Okporie
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Godwin Onyishi
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emeka Utobo
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Lynda Ekwu
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Senesie Swaray
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Momodu Jalloh
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
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Genetic Variation and Alleviation of Salinity Stress in Barley ( Hordeum vulgare L.). Molecules 2018; 23:molecules23102488. [PMID: 30274189 PMCID: PMC6222302 DOI: 10.3390/molecules23102488] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 11/19/2022] Open
Abstract
Barley (Hordeum vulgare L.) represents one of the most important cereals cultivated worldwide. Investigating genetic variability and structure of barley is important for enhancing the crop productivity. This study aimed to investigate the diversity and structure of 40 barley genotypes originated from three European countries (France, the Netherlands, Poland) using amplified fragment length polymorphisms (AFLPs). It also aimed to study 5-aminolevulinic acid (ALA) effect on salinity tolerance of six barley genotypes. The expected heterozygosity (He) diverged from 0.126 to 0.501, with a mean of 0.348. Polymorphic information content (PIC) diverged from 0.103 to 0.482 across barley genotypes, with a mean of 0.316, indicating that barley genotypes are rich in a considerable level of genetic diversity. The 40 barley genotypes were further studied based on their geographical origin (Western Europe and Eastern Europe). The Eastern European region (Poland) has a higher barley variability than the Western European region (France and the Netherlands). Nei’s distance-based cluster tree divided the 40 barley accessions into two major clusters; one cluster comprised all the varieties originated from the Eastern European region, while the other major cluster included all accessions originated from the Western European region. Structure analysis results were in a complete concordance with our cluster analysis results. Slaski 2, Damseaux and Urbanowicki genotypes have the highest diversity level, whereas Carmen, Bigo and Cambrinus genotypes have the lowest level. The response of these six varieties to NaCl stress was also investigated. Salt stress (100 mM NaCl) slightly decreased levels of chlorophyll, carotenoid and osmolytes (proteins, soluble sugars, phenolics and flavonoids) in the leaves of Slaski 2, Damseaux and Urbanowicki genotypes at non-significant level, as compared to control samples. However, pigment contents and osmolytes in leaves of Carmen, Bigo and Cambrinus genotypes were significantly decreased by salt stress. Antioxidant enzyme activities were significantly increased in Slaski 2 genotype, but non-significantly increased in Carmen by salt stress. Priming Slaski 2 and Carmen cultivars with ALA under salt stress significantly induced pigment contents, antioxidants enzymes activity and stress-responsive genes expression, relative to NaCl-stressed plants. In conclusion, this study suggested a correlation between variability percentage and degree of salinity resistance. ALA improved salt tolerance in barley.
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Superior adaptation of aerobic rice under drought stress in Iran and validation test of linked SSR markers to major QTLs by MLM analysis across two years. Mol Biol Rep 2018; 45:1037-1053. [PMID: 30014294 DOI: 10.1007/s11033-018-4253-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/10/2018] [Indexed: 01/22/2023]
Abstract
Drought is one of the biggest challenges for rice (Oryza sativa L.) production in rainfed areas. Developing "aerobic rice" cultivars could be a valuable alternative to irrigated/rainfed areas. During 2010-2013, 115 rice genotypes, including non-local cultivars and aerobic rice genotypes, were evaluated and 31 rice genotypes were screened, while 21 Iranian lowland rice cultivars (52 genotypes) were investigated under non-stress and drought conditions at the University of Guilan, Rasht, Iran, in 2014 and 2017. The results revealed the superiority of high yielding genotypes, namely Neda (6.202 t ha- 1), IR82639-B-B-140-1 (6.020 t ha- 1), and IR82635-B-B-82-2 (5.75 t ha- 1) under non-stress, Panda (4.512 t ha- 1), and IR82639-B-B-140-1 (4.08 t ha- 1), under drought stress conditions. Based on the molecular markers evaluation using identified SSR markers linked to major QTLs different important traits specially drought stress, IR 82639-B-B-140-1 showed the highest genetic distance with high-quality Iranian lowland cultivars, which could be considered as a donor for the development of new cultivars. Moreover, the assignment of rice genotypes based on Jaccard distance clustering was in agreement with the grouping of structure analysis. The validation test using MLM analysis in this natural population revealed the most important significant associations that were identified under drought conditions. These are: the associations between RM306, RM319, RM511, RM28166, and RM11943 with different grain yield (GY)-related traits simultaneously and stable across both years. These markers, which were verified in a natural population across 2 years, could be considered as the potential markers for use in marker-assisted breeding and to improve the grain yield of rice.
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Mathpal P, Kumar U, Kumar A, Kumar S, Malik S, Kumar N, Dhaliwal HS, Kumar S. Identification, expression analysis, and molecular modeling of Iron-deficiency-specific clone 3 ( Ids3)-like gene in hexaploid wheat. 3 Biotech 2018; 8:219. [PMID: 29666780 PMCID: PMC5899073 DOI: 10.1007/s13205-018-1230-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/23/2018] [Indexed: 12/21/2022] Open
Abstract
Graminaceous plants secrete hydroxylated phytosiderophores encoded by the genes iron-deficiency-specific clone 2 (Ids2) and iron-deficiency-specific clone 3 (Ids3). An effort was made to identify a putative ortholog of Hodeum vulgare Ids3 gene in hexaploid wheat. The protein structure of TaIDS3 was modeled using homology modeling and structural behavior of modeled structure was analyzed at 20 ns. The simulation trajectory using molecular dynamics simulation suggested the model to be stable with no large fluctuations in residues and local domain level RMSF values (< 2.4 Å). In addition, the ProFunc results also predict the functional similarity between the proteins of HvIDS3 and its wheat ortholog (TaIDS3). The TaIds3 gene was assigned to the telomeric region of chromosome arm 7AS which supports the results obtained through bioinformatics analysis. The relative expression analysis of TaIds3 indicated that the detectable expression of TaIds3 is induced after 5th day of Fe starvation and increases gradually up to 15th day, and thereafter, it decreases until 35th day of Fe-starvation. This reflects that Fe deficiency directly regulates the induction of TaIds3 in the roots of hexaploid wheat. The identification of HvIds3-like gene in wheat has opened up new opportunities to enhance the nutrient quality in wheat through biofortification program.
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Affiliation(s)
- Priyanka Mathpal
- Molecular Cytogenetics Laboratory, Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, Ch. Charan Singh Haryana Agricultural University, Hisar, Haryana 125004 India
| | - Anuj Kumar
- Advanced Centre for Computational and Applied Biotechnology, Uttarakhand Council for Biotechnology, Dehradun, Uttarakhand 248007 India
| | - Sanjay Kumar
- Centre for Bioinformatics, Biotech Park, Lucknow, Uttar Pradesh 226021 India
| | - Sachin Malik
- Molecular Cytogenetics Laboratory, Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Naveen Kumar
- Molecular Cytogenetics Laboratory, Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - H. S. Dhaliwal
- Akal School of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Sundip Kumar
- Molecular Cytogenetics Laboratory, Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
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William M, Dorocicz I, Kasha KJ. Use of Microsatellite DNA to Distinguish Malting and Nonmalting Barley Cultivars. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-55-0107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Manilal William
- Crop Science Department, University of Guelph, Guelph, N1G 2W1, ON, Canada
| | - Irene Dorocicz
- Crop Science Department, University of Guelph, Guelph, N1G 2W1, ON, Canada
| | - Ken J. Kasha
- Crop Science Department, University of Guelph, Guelph, N1G 2W1, ON, Canada
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Hoffman DL, Bregitzer P. Identification of Reproducible PCR-RAPD Markers that Enable the Differentiation of Closely Related Six-Rowed Malting Barley (Hordeum VulgareL.) Cultivars. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-54-0172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- David L. Hoffman
- U. S. Department of Agriculture, Agricultural Research Service, National Small Grains Germplasm Research Facility, Aberdeen, ID 83210
| | - Phil Bregitzer
- U. S. Department of Agriculture, Agricultural Research Service, National Small Grains Germplasm Research Facility, Aberdeen, ID 83210
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Lin Y, Liao M, Yang G, Yu W, Guan H, Fan W, Dong J. Identification of Barley Varieties Used in Beer Production by Microsatellite DNA Markers. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2007-0115-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yan Lin
- College of Marine Life Sciences, Ocean University of China, Qingdao, Peoples Republic of China
| | - Meijie Liao
- College of Marine Life Sciences, Ocean University of China, Qingdao, Peoples Republic of China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Peoples Republic of China
| | - Wengong Yu
- Institute of Marine Drugs and Food, Ocean University of China, Qingdao, Peoples Republic of China
| | - Huashi Guan
- Institute of Marine Drugs and Food, Ocean University of China, Qingdao, Peoples Republic of China
| | - Wei Fan
- Department of Technology, Center of Research and Development, Tsingtao Brewery Co. Ltd., Qingdao, Peoples Republic of China
| | - Jianjun Dong
- Department of Technology, Center of Research and Development, Tsingtao Brewery Co. Ltd., Qingdao, Peoples Republic of China
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Sydenham SL, Barnard A. Targeted Haplotype Comparisons between South African Wheat Cultivars Appear Predictive of Pre-harvest Sprouting Tolerance. FRONTIERS IN PLANT SCIENCE 2018; 9:63. [PMID: 29449853 PMCID: PMC5799232 DOI: 10.3389/fpls.2018.00063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/12/2018] [Indexed: 05/06/2023]
Abstract
Pre-harvest sprouting (PHS) has been a serious production constraint for over two decades, especially in the summer rainfall wheat production regions of South Africa. It is a complex genetic trait controlled by multiple genes, which are significantly influenced by environmental conditions. This complicates the accurate prediction of a cultivar's stability in terms of PHS tolerance. A number of reports have documented the presence of major QTL on chromosomes 3A and 4A of modern bread wheat cultivars, which confer PHS tolerance. In this study, the SSR marker haplotype combination of chromosomes 3A and 4A of former and current South African cultivars were compared with the aim to select for improved PHS tolerance levels in future cultivars. A total of 101 wheat cultivars, including a susceptible cultivar and five international tolerant sources, were used in this study. These cultivars and donors were evaluated for their PHS tolerance by making use of a rain simulator. In addition, five seeds of each entry were planted out into seedling trays and leaf material harvested for DNA isolation. A modified CTAB extraction method was used before progressing to downstream PCR applications. Eight SSR markers targeted from the well-characterized 3A and 4A QTL regions associated with PHS tolerance, were used to conduct targeted haplotype analysis. Additionally, recently published KASP SNP markers, which identify the casual SNP mutations within the TaPHS1 gene, were used to genotype the germplasm. The haplotype marker data and phenotypic PHS data were compared across all cultivars and different production regions. A relative change in observed phenotypic variation percentage was obtained per marker allele and across marker haplotype combinations when compared to the PHS susceptible cultivar, Tugela-DN. Clear favorable haplotypes, contributing 40-60% of the variation for PHS tolerance, were identified for QTL 3A and 4A. Initial analyses show haplotype data appear to be predictive of PHS tolerance status and germplasm can now be selected to improve PHS tolerance. These haplotype data are the first of its kind for PHS genotyping in South Africa. In future, this can be used as a tool to predict the possible PHS tolerance range of a new cultivar.
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Keller J, Rousseau-Gueutin M, Martin GE, Morice J, Boutte J, Coissac E, Ourari M, Aïnouche M, Salmon A, Cabello-Hurtado F, Aïnouche A. The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus. DNA Res 2017; 24:343-358. [PMID: 28338826 PMCID: PMC5737547 DOI: 10.1093/dnares/dsx006] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/02/2017] [Indexed: 01/21/2023] Open
Abstract
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades.
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Affiliation(s)
- J Keller
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - M Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.,IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France
| | - G E Martin
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
| | - J Morice
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France
| | - J Boutte
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - E Coissac
- Laboratoire d'Ecologie Alpine, CNRS - Université de Grenoble 1 - Université de Savoie, 38041 Grenoble, France
| | - M Ourari
- Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie, Université Abderrahmane Mira, 06000 Bejaia, Algeria
| | - M Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - F Cabello-Hurtado
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
| | - A Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France
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A novel in vitro transformation of Lepidium draba L. using rapid direct shoot regeneration. 3 Biotech 2017; 7:284. [PMID: 28828291 DOI: 10.1007/s13205-017-0915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022] Open
Abstract
The present research is carried out to study Lepidium draba gene transformation for the first time, using direct shoot explants. As a prerequisite for gene transformation, the regeneration conditions in L. draba were optimized. We achieved an efficient and reproducible protocol for successful direct shoot regeneration without intervening callus formation. The results indicate that L. draba is the insistent species of Brassicaceae in direct shoot regeneration. Various explants of L. draba were genetically transformed with different strains of Agrobacterium tumefaciens, viz., LBA4404, GV3850, GV3101, and EHA105, using the vector pBI121. Expression of GUS reporter protein was assayed by histochemical staining. In addition, using the PCR method with specific primers proved the integration of GUS gene into the plants. The highest transformation efficiency was achieved with Agrobacterium strain GV3850. Moreover, we found that infected hypocotyl and root explants of L. draba interestingly yielded higher transformation efficiency, so that in hypocotyls on average exceeded 70% of the explants. This study showed that L. draba, in addition to the numerous desirable traits, has a high potential for gene transfer.
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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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Bansal M, Kaur S, Dhaliwal HS, Bains NS, Bariana HS, Chhuneja P, Bansal UK. Mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance loci in wheat. PLANT PATHOLOGY 2017; 66:38-44. [PMID: 0 DOI: 10.1111/ppa.12549] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- M. Bansal
- School of Agricultural Biotechnology; Punjab Agricultural University; Ludhiana Punjab 141 004 India
| | - S. Kaur
- School of Agricultural Biotechnology; Punjab Agricultural University; Ludhiana Punjab 141 004 India
| | - H. S. Dhaliwal
- School of Agricultural Biotechnology; Punjab Agricultural University; Ludhiana Punjab 141 004 India
| | - N. S. Bains
- Department of Plant Breeding and Genetics; Punjab Agricultural University; Ludhiana Punjab 141 004 India
| | - H. S. Bariana
- University of Sydney Plant Breeding Institute-Cobbitty; PMB 4011 Narellan NSW 2567 Australia
| | - P. Chhuneja
- School of Agricultural Biotechnology; Punjab Agricultural University; Ludhiana Punjab 141 004 India
| | - U. K. Bansal
- University of Sydney Plant Breeding Institute-Cobbitty; PMB 4011 Narellan NSW 2567 Australia
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Ashraf H, Husaini AM, Ashraf Bhat M, Parray GA, Khan S, Ganai NA. SSR based genetic diversity of pigmented and aromatic rice ( Oryza sativa L.) genotypes of the western Himalayan region of India. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:547-555. [PMID: 27924127 PMCID: PMC5120034 DOI: 10.1007/s12298-016-0377-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 09/01/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
A set of 24 of SSR markers were used to estimate the genetic diversity in 16 rice genotypes found in Western Himalayas of Kashmir and Himachal Pradesh, India. The level of polymorphism among the genotypes of rice was evaluated from the number of alleles and PIC value for each of the 24 SSR loci. A total of 68 alleles were detected across the 16 genotypes through the use of these 24 SSR markers The number of alleles per locus generated varied from 2 (RM 338, RM 452, RM 171) to 6 (RM 585, RM 249, RM 481, RM 162). The PIC values varied from 0.36 (RM 1) to 0.86 (RM 249) with an average of 0.62 per locus. Based on information generated, the genotypes got separated in six different clusters. Cluster 1 comprised of 4 genotypes viz; Zag 1, Zag 13, Pusa sugandh 3, and Zag 14, separated from each other at a similarity value of 0.40. Cluster second comprised of 3 landraces viz; Zag 2. Zag 4 and Zag10 separated from each other at a similarity value of 0.45. Cluster third comprised of 3 genotypes viz; Grey rice, Mushk budji and Kamad separated from each other at a similarity value of 0.46. Cluster fourth had 2 landraces viz; Kawa kreed and Loual anzul, and was not sub clustered. Fifth cluster had 3 genotypes viz; Zag 12, Purple rice and Jhelum separated from each other at a similarity value of 0.28. Cluster 6 comprised of a single popular variety i.e. Shalimar rice 1 with independent lineage.
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Affiliation(s)
- Humaira Ashraf
- Centre for Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir India
| | - Amjad M. Husaini
- Centre for Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir India
| | - M. Ashraf Bhat
- Centre for Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir India
| | - GA Parray
- Mountain Research Centre for Field Crops, Khudwani, Anantnag, Jammu and Kashmir India
| | - Salim Khan
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Nazir A. Ganai
- Centre for Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir India
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SSR ANALYSIS IN THE STUDY OF GENETIC DIVERSITY AND SIMILARITY OF BARLEY CULTIVARS. BIOTECHNOLOGIA ACTA 2016. [DOI: 10.15407/biotech9.03.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Mieuzet L, Quillévéré A, Pilet ML, Le May C. Development and characterization of microsatellite markers for the oomyceta Aphanomyces euteiches. Fungal Genet Biol 2016; 91:1-5. [PMID: 26964907 DOI: 10.1016/j.fgb.2016.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 03/02/2016] [Accepted: 03/05/2016] [Indexed: 11/30/2022]
Abstract
Aphanomyces euteiches Drechsler is a serious pathogen of leguminous crops that causes devastating root rot of pea worldwide. Given that A. euteiches is a diploid organism, robust, codominant markers are needed for population genetics studies. We have developed and screened a microsatellite-enriched small-insert genomic library for identification of A. euteiches SSR containing sequences. Fourteen out of the 48 primer pairs designed to amplify SSR, produced unambiguous polymorphic products in our test population of 94 isolates. The number of alleles at each locus ranged from one to four. The identification of new markers would enhance the ability to evaluate the genetic structure of A. euteiches populations, and pathogen evolution.
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Affiliation(s)
- Lucie Mieuzet
- INRA, UMR1349 Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, 35653 Le Rheu, France; Agrocampus Ouest, Laboratoire Ecologie et Santé des Plantes (ESP), 65 rue de Saint Brieuc, 35042 Rennes, France
| | - A Quillévéré
- INRA, UMR1349 Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, 35653 Le Rheu, France; Agrocampus Ouest, Laboratoire Ecologie et Santé des Plantes (ESP), 65 rue de Saint Brieuc, 35042 Rennes, France
| | - M L Pilet
- INRA, UMR1349 Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, 35653 Le Rheu, France; Agrocampus Ouest, Laboratoire Ecologie et Santé des Plantes (ESP), 65 rue de Saint Brieuc, 35042 Rennes, France
| | - C Le May
- INRA, UMR1349 Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, 35653 Le Rheu, France; Agrocampus Ouest, Laboratoire Ecologie et Santé des Plantes (ESP), 65 rue de Saint Brieuc, 35042 Rennes, France; Université de Rennes I, 9 rue Jean Macé, 35700 Rennes, France.
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Wu XL, Wang JW, Cheng YK, Ye XL, Li W, Pu ZE, Jiang QT, Wei YM, Deng M, Zheng YL, Chen GY. Inheritance and Molecular Mapping of an All-Stage Stripe Rust Resistance Gene Derived from the Chinese Common Wheat Landrace "Yilongtuomai". J Hered 2016; 107:463-70. [PMID: 27208148 DOI: 10.1093/jhered/esw032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
Yellow or stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating foliar disease that affects common wheat (Triticum aestivum L.) around the world. In China, common wheat landraces are potential sources of disease and abiotic stress resistance genes for wheat improvement. Yilongtuomai (YL), a wheat landrace from Yilong County, Sichuan Province, shows high levels of resistance against most Chinese Pst races. In this study, the resistance of YL to stripe rust disease was examined in detail. Parent strains, YL and Taichung 29, a variety susceptible to Pst race CYR32, and their F1, F2, and F2:3 offspring, were inoculated with CYR32 during the seedling stage in the field or adult-plant stage in the greenhouse. Results indicated that resistance to CYR32 in YL is conferred by a single dominant gene, designated YrYL The segregating F2 population (352 plants), was analyzed in terms of its resistance locus using simple sequence repeats (SSRs), resistance gene analog polymorphisms (RGAPs), and sequence-related amplified polymorphism (SRAP). A linkage group of 6 SSRs, 2 RGAPs, and 1 SRAP was constructed for the YrYL gene. Using the identified SSRs associated with physical mapping of RGAP using Chinese Spring nullisomic-tetrasomic stocks, the YrYL gene was localized to the short arm of chromosome 7D. The gene was flanked by 1 SSR marker, Xbarc92, and 1 RGAP marker, CLRRfor/Ptokin4, at genetic distances of 5.35 and 9.86 cM, respectively. The YrYL gene was compared to other stripe rust resistance genes reported on chromosome 7D by evaluating its reaction patterns to CYR32 and its pedigree relationship. Our results suggest that the YrYL gene is a new stripe rust resistance gene.
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Affiliation(s)
- Xue-Lian Wu
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Jian-Wei Wang
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Yu-Kun Cheng
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Xue-Ling Ye
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Wei Li
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Zhi-En Pu
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Qian-Tao Jiang
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Yu-Ming Wei
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Mei Deng
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - You-Liang Zheng
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu)
| | - Guo-Yue Chen
- From the Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Wu, Wang, Cheng, Ye, Jiang, Li, Deng, Zheng, and Chen); Key Laboratory of Crop Germplasm Resources Utilization in Southwest China, Ministry of Agriculture, Sichuan Agricultural University, Ya'an, Sichuan 625014, People's Republic of China (Wei and Zheng); College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, People's Republic of China (Li and Pu).
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Ferreira JR, Pereira JF, Turchetto C, Minella E, Consoli L, Delatorre CA. Assessment of genetic diversity in Brazilian barley using SSR markers. Genet Mol Biol 2016; 39:86-96. [PMID: 27007902 PMCID: PMC4807376 DOI: 10.1590/1678-4685-gmb-2015-0148] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/25/2015] [Indexed: 11/22/2022] Open
Abstract
Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs.
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Affiliation(s)
- Jéssica Rosset Ferreira
- Departamento de Plantas de Lavoura, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | | | | | | | - Carla Andréa Delatorre
- Departamento de Plantas de Lavoura, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Bian M, Jin X, Broughton S, Zhang XQ, Zhou G, Zhou M, Zhang G, Sun D, Li C. A new allele of acid soil tolerance gene from a malting barley variety. BMC Genet 2015. [PMID: 26219378 PMCID: PMC4518660 DOI: 10.1186/s12863-015-0254-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Background Acid soil is a serious limitation to crop production all over the world. Toxic aluminium (Al) cations in acid soil inhibit root growth and reduce yield. Although a gene tolerant to acid soil has been identified, it has not been used in malting barley breeding, which is partly due to the acid soil tolerance gene being linked to unfavorable malting quality traits. Results A Brazilian malting barley variety Br2 was identified as tolerant to acid soil. A doubled haploid (DH) population was developed from a cross between Br2 and the Australian acid-sensitive cultivar Hamelin. The DH population was tested for acid soil tolerance in native acid soil and a hydroponic system with pH 4.2, pH 4.2 + Al or pH 6.5, and genotyped using SSR, DArT and gene-specific markers. A single QTL was detected for all parameters related to acid soil tolerance. The QTL was mapped to the known HvMATE location on chromosome 4H. Sequence alignment of the HvMATE gene identified 13 INDELs and 87 SNPs, where one SNP coded for a single amino acid difference between the two varieties. A gene-specific marker was developed to detect the single nucleotide polymorphism between Hamelin and Br2. This marker co-segregated with aluminium tolerance and accounted for 79 % of phenotypic variation for acid soil tolerance. Conclusion The present study identified a novel source of acid soil/Al tolerance from a Brazilian malting barley cultivar Br2. This variety tolerated Al toxicity but was sensitive to low pH which is similar to most other Al-tolerant varieties. A gene-specific marker Cit7 was developed based on the HvMATE gene sequence. Cit7 will improve the efficiency of molecular-assisted selection of new barley varieties with tolerance to acid soil. Multiple alleles exist for the acid soil tolerance gene on chromosome 4H, so a malting barley variety that tolerates acid soil could be developed by selecting suitable tolerant alleles. Tolerance to low pH may play an important role for barley to adapt to acid soils. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0254-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miao Bian
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. .,Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Xiaoli Jin
- Agronomy Department, Zhejiang University, Hangzhou, China.
| | - Sue Broughton
- Department of Agriculture & Food WA, 3 Baron-Hay Court, South Perth, WA, 6155, Australia.
| | - Xiao-Qi Zhang
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Gaofeng Zhou
- Department of Agriculture & Food WA, 3 Baron-Hay Court, South Perth, WA, 6155, Australia.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, P.O. Box 46, Kings Meadows, TAS, 7249, Australia.
| | - Guoping Zhang
- Agronomy Department, Zhejiang University, Hangzhou, China.
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Chengdao Li
- Department of Agriculture & Food WA, 3 Baron-Hay Court, South Perth, WA, 6155, Australia. .,Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, 6150, Australia.
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Identification and mapping stripe rust resistance gene YrLM168a using extreme individuals and recessive phenotype class in a complicate genetic background. Mol Genet Genomics 2015; 290:2271-8. [PMID: 26113523 DOI: 10.1007/s00438-015-1077-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 06/04/2015] [Indexed: 10/23/2022]
Abstract
The identification and characterization of resistance genes effective against stripe rust of wheat is beneficial for modern wheat breeding programs. Molecular markers to such genes facilitate their deployment. The variety Milan has resistance that is effective against the predominant stripe rust races in the Sichuan region. Two resistant and two susceptible F8 lines from a cross between Milan and the susceptible variety Chuannong 16 were used to investigate inheritance of the Milan resistance. Three F2 populations were developed from crosses between the resistant lines and their susceptible sibling lines (LM168a × LM168c, LM168c × LM168a, LM168b × LM168d) and used for genetic analysis and molecular mapping of the genes for resistance. The stripe rust resistance in LM168a and LM168b was conferred by a single dominant gene, temporarily designated as YrLM168a. Forty-five extreme susceptible plants from the F2 families of LM168d × LM168b were genotyped with 836 simple sequence repeat (SSR) markers to map YrLM168a. YrLM168a was mapped in chromosome 6BL. The nearest flanking markers Xwmc756 and Xbarc146 were 4.6 and 4.6 cM away from the gene at both sides, respectively. The amplification results of twenty extreme resistant (IT 0) and susceptible (IT 4) F2 plants of LM168c × LM168a and LM168a × LM168c with marker Xwmc756 further validated the mapping results. The study suggested that extreme individuals and recessive phenotype class can be successfully used for mapping genes, which should be efficient and reliable. In addition, the flanking markers near YrLM168a should be helpful in marker-assisted breeding.
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Jaiswal V, Gahlaut V, Mathur S, Agarwal P, Khandelwal MK, Khurana JP, Tyagi AK, Balyan HS, Gupta PK. Identification of Novel SNP in Promoter Sequence of TaGW2-6A Associated with Grain Weight and Other Agronomic Traits in Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0129400. [PMID: 26076351 PMCID: PMC4468092 DOI: 10.1371/journal.pone.0129400] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 05/07/2015] [Indexed: 11/18/2022] Open
Abstract
TaGW2 is an orthologue of rice gene OsGW2, which encodes E3 RING ubiquitin ligase and controls the grain size in rice. In wheat, three copies of TaGW2 have been identified and mapped on wheat homoeologous group 6 viz. TaGW2-6A, TaGW2-6B and TaGW2-6D. In the present study, using as many as 207 Indian wheat genotypes, we identified four SNPs including two novel SNPs (SNP-988 and SNP-494) in the promoter sequence of TaGW2-6A. All the four SNPs were G/A or A/G substitutions (transitions). Out of the four SNPs, SNP-494 was causal, since it was found associated with grain weight. The mean TGW (41.1 g) of genotypes with the allele SNP-494_A was significantly higher than mean TGW (38.6 g) of genotypes with the allele SNP-494_G. SNP-494 also regulates the expression of TaGW2-6A so that the wheat genotypes with SNP-494_G have higher expression and lower TGW and the genotypes with SNP-494_A have lower expression but higher TGW. Besides, SNP-494 was also found associated with grain length-width ratio, awn length, spike length, grain protein content, peduncle length and plant height. This suggested that gene TaGW2-6A not only controls grain size, but also controls other agronomic traits. In the promoter region, SNP-494 was present in 'CGCG' motif that plays an important role in Ca2+/calmodulin mediated regulation of genes. A user-friendly CAPS marker was also developed to identify the desirable allele of causal SNP (SNP-494) for use in marker-assisted selection for improvement of grain weight in wheat. Using four SNPs, five haplotypes were identified; of these, Hap_5 (G_A_G_A) was found to be a desirable haplotype having significantly higher grain weight (41.13g) relative to other four haplotypes (36.33-39.16 g).
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Affiliation(s)
- Vandana Jaiswal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vijay Gahlaut
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Saloni Mathur
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi, India
| | - Priyanka Agarwal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | | | - Jitendra Paul Khurana
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- * E-mail:
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Dawson IK, Russell J, Powell W, Steffenson B, Thomas WTB, Waugh R. Barley: a translational model for adaptation to climate change. THE NEW PHYTOLOGIST 2015; 206:913-931. [PMID: 25605349 DOI: 10.1111/nph.13266] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/06/2014] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes - including examples that are indicative of the complexities involved in designing appropriate responses - are presented, and key developments for the future highlighted.
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Affiliation(s)
- Ian K Dawson
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Joanne Russell
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Wayne Powell
- CGIAR Consortium Office, Montpellier Cedex 5, France
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - William T B Thomas
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute (JHI), Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, College of Life Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
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Genetic diversity and population structure in a legacy collection of spring barley landraces adapted to a wide range of climates. PLoS One 2014; 9:e116164. [PMID: 25541702 PMCID: PMC4277474 DOI: 10.1371/journal.pone.0116164] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 12/04/2014] [Indexed: 01/09/2023] Open
Abstract
Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type – and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches.
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Ren X, Wang Y, Yan S, Sun D, Sun G. Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley. Genome 2014; 57:239-44. [PMID: 25033083 DOI: 10.1139/gen-2014-0039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.
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Affiliation(s)
- Xifeng Ren
- a College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Angeles-Shim RB, Vinarao RB, Marathi B, Jena KK. Molecular analysis of Oryza latifolia Desv. (CCDD genome)-derived introgression lines and identification of value-added traits for rice (O. sativa L.) improvement. J Hered 2014; 105:676-89. [PMID: 24939891 DOI: 10.1093/jhered/esu032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Oryza latifolia is a tetraploid wild Oryza species with a CCDD genome that has been reported to harbor resistance to bacterial blight (BB), brown planthopper, and whitebacked planthopper. Aside from these traits, O. latifolia is also being tapped as a new source of resistance to lodging and high biomass production. To explore the genetic potential of O. latifolia as a novel genetic resource for the improvement of existing O. sativa cultivars, 27 disomic derivatives of O. latifolia monosomic alien addition lines (MAAL) were characterized for alien chromosome segment introgressions and evaluated for yield components, BB resistance, and strong stem characteristics. A total of 167 simple sequence repeat, sequence tagged site, and single nucleotide polymorphism markers, along with newly developed indel markers that were specifically designed to detect O. latifolia chromosome segment introgressions in an O. sativa background, were used to define alien introgressions in 27 disomics derived from O. latifolia MAALs. Genotype data showed that 32 unique introgressions spanning 0.31-22.73 Mb were introgressed in different combinations in each of the 27 disomic derivatives. Evaluation of the disomic derivatives for agronomic traits identified lines with putative QTLs for resistance to Philippine races 3A, 4, 9A, and 9D of BB. Putative quantitative trait loci (QTLs) conferring strong stem in 19 out of the 27 disomic derivatives studied were also identified from O. latifolia introgressions on chromosome 6.
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Affiliation(s)
- Rosalyn B Angeles-Shim
- From the Novel Gene Resources Laboratory, Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines (Angeles-Shim, Vinarao, Marathi, and Jena); and the Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan (Angeles-Shim)
| | - Ricky B Vinarao
- From the Novel Gene Resources Laboratory, Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines (Angeles-Shim, Vinarao, Marathi, and Jena); and the Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan (Angeles-Shim)
| | - Balram Marathi
- From the Novel Gene Resources Laboratory, Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines (Angeles-Shim, Vinarao, Marathi, and Jena); and the Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan (Angeles-Shim)
| | - Kshirod K Jena
- From the Novel Gene Resources Laboratory, Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines (Angeles-Shim, Vinarao, Marathi, and Jena); and the Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan (Angeles-Shim).
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