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Sallam A, Awadalla RA, Elshamy MM, Börner A, Heikal YM. Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population. Comput Struct Biotechnol J 2024; 23:870-882. [PMID: 38356657 PMCID: PMC10864764 DOI: 10.1016/j.csbj.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.
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Affiliation(s)
- Ahmed Sallam
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Rawan A. Awadalla
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Maha M. Elshamy
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Andreas Börner
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
| | - Yasmin M. Heikal
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
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Guppy JL, Jones DB, Kjeldsen SR, Le Port A, Khatkar MS, Wade NM, Sellars MJ, Steinig EJ, Raadsma HW, Jerry DR, Zenger KR. Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs. BMC Genomics 2020; 21:541. [PMID: 32758142 DOI: 10.1186/s12864-020-06960-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/29/2020] [Indexed: 11/26/2022] Open
Abstract
Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.
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Yao F, Zhang X, Ye X, Li J, Long L, Yu C, Li J, Wang Y, Wu Y, Wang J, Jiang Q, Li W, Ma J, Wei Y, Zheng Y, Chen G. Characterization of molecular diversity and genome-wide association study of stripe rust resistance at the adult plant stage in Northern Chinese wheat landraces. BMC Genet 2019; 20:38. [PMID: 30914040 PMCID: PMC6434810 DOI: 10.1186/s12863-019-0736-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/03/2019] [Indexed: 12/02/2022] Open
Abstract
Background Stripe rust is a serious fungal disease of wheat (Triticum aestivum L.) caused by Puccinia striiformis f. sp. tritici (Pst), which results in yield reduction and decreased grain quality. Breeding for genetic resistance to stripe rust is the most cost-effective method to control the disease. In the present study, a genome-wide association study (GWAS) was conducted to identify markers linked to stripe rust resistance genes (or loci) in 93 Northern Chinese wheat landraces, using Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) molecular marker technology based on phenotypic data from two field locations over two growing seasons in China. Results Seventeen accessions were verified to display stable and high levels of adult plant resistance (APR) to stripe rust via multi-environment field assessments. Significant correlations among environments and high heritability were observed for stripe rust infection type (IT) and disease severity (DS). Using mixed linear models (MLM) for the GWAS, a total of 32 significantly associated loci (P < 0.001) were detected. In combination with the linkage disequilibrium (LD) decay distance (6.4 cM), 25 quantitative trait loci (QTL) were identified. Based on the integrated map of previously reported genes and QTL, six QTL located on chromosomes 4A, 6A and 7D were mapped far from resistance regions identified previously, and represent potentially novel stripe rust resistance loci at the adult plant stage. Conclusions The present findings demonstrated that identification of genes or loci linked to significant markers in wheat by GWAS is feasible. Seventeen elite accessions conferred with stable and high resistance to stripe rust, and six putative newly detected APR loci were identified among the 93 Northern Chinese wheat landraces. The results illustrate the potential for acceleration of molecular breeding of wheat, and also provide novel sources of stripe rust resistance with potential utility in the breeding of improved wheat cultivars. Electronic supplementary material The online version of this article (10.1186/s12863-019-0736-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fangjie Yao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Xuemei Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Li Long
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Can Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuqi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yu Wu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.,State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.,State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.,State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China. .,State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, People's Republic of China.
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Dresvyannikova AE, Watanabe N, Muterko AF, Krasnikov AA, Goncharov NP, Dobrovolskaya OB. Characterization of a dominant mutation for the liguleless trait: Aegilops tauschii liguleless (Lg t). BMC Plant Biol 2019; 19:55. [PMID: 30813900 PMCID: PMC6393956 DOI: 10.1186/s12870-019-1635-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Leaves of Poaceae have a unique morphological feature: they consist of a proximal sheath and a distal blade separated by a ligular region. The sheath provides structural support and protects young developing leaves, whereas the main function of the blade is photosynthesis. The auricles allow the blade to tilt back for optimal photosynthesis and determine the angle of a leaf, whereas the ligule protects the stem from the entry of water, microorganisms, and pests. Liguleless variants have an upright leaf blade that wraps around the culm. Research on liguleless mutants of maize and other cereals has led to identification of genes that are involved in leaf patterning and differentiation. RESULTS We characterized an induced liguleless mutant (LM) of Aegilops tauschii Coss., a donor of genome D of bread wheat Triticum aestivum L.. The liguleless phenotype of LM is under dominant monogenic control (Lgt). To determine precise position of Lgt on the Ae. tauschii genetic map, highly saturated genetic maps were constructed containing 887 single-nucleotide polymorphism (SNP) markers derived via diversity arrays technology (DArT)seq. The Lgt gene was mapped to chromosome 5DS. Taking into account coordinates of the SNP markers, flanking Lgt, on the pseudomolecule 5D, a chromosomal region that contains this gene was determined, and a list of candidate genes was identified. Morphological features of the LM phenotype suggest that Lgt participates in the control of leaf development, mainly, in leaf proximal-distal patterning, and its dominant mutation causes abnormal ligular region but does not affect reproductive development. CONCLUSIONS Here we report characterization of a liguleless Ae. tauschii mutant, whose phenotype is under control of a dominant mutation of Lgt. The dominant mode of inheritance of the liguleless trait in a Triticeae species is reported for the first time. The position of the Lgt locus on chromosome 5DS allowed us to identify a list of candidate genes. This list does not contain Ae. tauschii orthologs of any well-characterized cereal genes whose mutations cause liguleless phenotypes. Thus, the characterized Lgt mutant represents a new model for further investigation of plant leaf patterning and differentiation.
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Affiliation(s)
- Alina E. Dresvyannikova
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090 Russia
| | | | - Alexander F. Muterko
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
| | - Alexander A. Krasnikov
- Central Siberian Botanical Garden SB RAS, Zolotodolinskaya Str., 101, Novosibirsk, 630090 Russia
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
| | - Oxana B. Dobrovolskaya
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090 Russia
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Valdisser PAMR, Pereira WJ, Almeida Filho JE, Müller BSF, Coelho GRC, de Menezes IPP, Vianna JPG, Zucchi MI, Lanna AC, Coelho ASG, de Oliveira JP, Moraes ADC, Brondani C, Vianello RP. In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping. BMC Genomics 2017; 18:423. [PMID: 28558696 PMCID: PMC5450071 DOI: 10.1186/s12864-017-3805-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/17/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs. RESULTS Using this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp. CONCLUSIONS For common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.
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Affiliation(s)
- Paula A. M. R. Valdisser
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Wendell J. Pereira
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | - Jâneo E. Almeida Filho
- Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Rio de Janeiro, RJ Brazil
| | - Bárbara S. F. Müller
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasília, DF Brazil
| | | | - Ivandilson P. P. de Menezes
- Laboratório de Genética e Biologia Molecular, Departamento de Biologia, Instituto Federal Goiano (IF Goiano), Urutaí, GO Brazil
| | - João P. G. Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Maria I. Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Anna C. Lanna
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | | | | | | | - Claudio Brondani
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
| | - Rosana P. Vianello
- Embrapa Arroz e Feijão (CNPAF), Santo Antônio de Goiás, Goiânia, GO Brazil
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