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Khan SU, Saeed S, Khan MHU, Fan C, Ahmar S, Arriagada O, Shahzad R, Branca F, Mora-Poblete F. Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed. Biomolecules 2021; 11:1516. [PMID: 34680149 PMCID: PMC8533950 DOI: 10.3390/biom11101516] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits.
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Affiliation(s)
- Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (S.U.K.); (S.S.); (M.H.U.K.)
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
| | - Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile;
| | - Raheel Shahzad
- Department of Biotechnology, Faculty of Science & Technology, Universitas Muhammadiyah Bandung, Bandung 40614, Indonesia;
| | - Ferdinando Branca
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3465548, Chile;
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Almerekova S, Genievskaya Y, Abugalieva S, Sato K, Turuspekov Y. Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data. PLANTS 2021; 10:plants10102025. [PMID: 34685834 PMCID: PMC8540147 DOI: 10.3390/plants10102025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/17/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022]
Abstract
The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson’s correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.
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Affiliation(s)
- Shyryn Almerekova
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (Y.G.); (S.A.)
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (Y.G.); (S.A.)
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (Y.G.); (S.A.)
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan;
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (S.A.); (Y.G.); (S.A.)
- Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
- Correspondence:
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Yermekbayev K, Griffiths S, Chhetry M, Leverington-Waite M, Orford S, Amalova A, Abugalieva S, Turuspekov Y. Construction of a Genetic Map of RILs Derived from Wheat (T. aestivum L.) Varieties Pamyati Azieva × Paragon Using High-Throughput SNP Genotyping Platform KASP—Kompetitive Allele Specific PCR. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542009015x] [Citation(s) in RCA: 2] [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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Li Z, Lhundrup N, Guo G, Dol K, Chen P, Gao L, Chemi W, Zhang J, Wang J, Nyema T, Dawa D, Li H. Characterization of Genetic Diversity and Genome-Wide Association Mapping of Three Agronomic Traits in Qingke Barley ( Hordeum Vulgare L.) in the Qinghai-Tibet Plateau. Front Genet 2020; 11:638. [PMID: 32719715 PMCID: PMC7351530 DOI: 10.3389/fgene.2020.00638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/26/2020] [Indexed: 12/18/2022] Open
Abstract
Barley (Hordeum vulgare L.) is one of the most important cereal crops worldwide. In the Qinghai-Tibet Plateau, six-rowed hulless (or naked) barley, called “qingke” in Chinese or “nas” in Tibetan, is produced mainly in Tibet. The complexity of the environment in the Qinghai-Tibet Plateau has provided unique opportunities for research on the breeding and adaptability of qingke barley. However, the genetic architecture of many important agronomic traits for qingke barley remains elusive. Heading date (HD), plant height (PH), and spike length (SL) are three prominent agronomic traits in barley. Here, we used genome-wide association (GWAS) mapping and GWAS with eigenvector decomposition (EigenGWAS) to detect quantitative trait loci (QTL) and selective signatures for HD, PH, and SL in a collection of 308 qingke barley accessions. The accessions were genotyped using a newly-developed, proprietary genotyping-by-sequencing (tGBS) technology, that yielded 14,970 high quality single nucleotide polymorphisms (SNPs). We found that the number of SNPs was higher in the varieties than in the landraces, which suggested that Tibetan varieties and varieties in the Tibetan area may have originated from different landraces in different areas. We have identified 62 QTLs associated with three important traits, and the observed phenotypic variation is well-explained by the identified QTLs. We mapped 114 known genes that include, but are not limited to, vernalization, and photoperiod genes. We found that 83.87% of the identified QTLs are located in the non-coding regulatory regions of annotated barley genes. Forty-eight of the QTLs are first reported here, 28 QTLs have pleotropic effects, and three QTL are located in the regions of the well-characterized genes HvVRN1, HvVRN3, and PpD-H2. EigenGWAS analysis revealed that multiple heading-date-related loci bear signatures of selection. Our results confirm that the barley panel used in this study is highly diverse, and showed a great promise for identifying the genetic basis of adaptive traits. This study should increase our understanding of complex traits in qingke barley, and should facilitate genome-assisted breeding for qingke barley improvement.
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Affiliation(s)
- Zhiyong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Namgyal Lhundrup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kar Dol
- Tibet Agricultural and Animal Husbandry College, Nyingchi, China
| | - Panpan Chen
- Tibet Agricultural and Animal Husbandry College, Nyingchi, China
| | - Liyun Gao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Wangmo Chemi
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tashi Nyema
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Dondrup Dawa
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Academy of Agriculture and Animal Sciences, Lhasa, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Anuarbek S, Abugalieva S, Pecchioni N, Laidò G, Maccaferri M, Tuberosa R, Turuspekov Y. Quantitative trait loci for agronomic traits in tetraploid wheat for enhancing grain yield in Kazakhstan environments. PLoS One 2020; 15:e0234863. [PMID: 32574201 PMCID: PMC7310741 DOI: 10.1371/journal.pone.0234863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/03/2020] [Indexed: 12/02/2022] Open
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) is one of the top crops in Kazakhstan, where it is cultivated in different ecological niches, mainly at higher latitudes in the steppe zone of the northern region. Therefore, local breeding programs for durum wheat are primarily focused on selection for high productivity in Northern Kazakhstan based on the introduction of promising foreign germplasm and the adoption of marker-assisted selection. In this study, a world tetraploid wheat collection consisted of 184 primitive and domesticated accessions, which were previously genotyped using 16,425 polymorphic SNP markers, was field-tested in Northern and South-eastern Kazakhstan. The field tests have allowed the identification of 80 durum wheat promising lines in Northern Kazakhstan in comparison with a local standard cultivar. Also, GGE (Genotype and Genotype by Environment) biplot analyses for yield performance revealed that accessions of T. dicoccum, T. carthlicum, and T. turanicum also have potential to improve durum wheat yield in the region. The genome-wide association study (GWAS) has allowed the identification of 83 MTAs (marker-trait associations) for heading date, seed maturation time, plant height, spike length, number of fertile spikes, number of kernels per spike, and thousand kernel weight. The comparison of the 83 identified MTAs with those previously reported in GWAS for durum wheat suggests that 38 MTAs are presumably novel, while the co-localization of a large number of MTAs with those previously published confirms the validity of the results of this study. The MTAs reported herewith will provide the opportunity to implement marker-assisted selection in ongoing durum wheat breeding projects targeting higher productivity in the region.
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Affiliation(s)
- Shynar Anuarbek
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Kazakh National Agrarian University, Almaty, Kazakhstan
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, CREA, Foggia, Italy
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, CREA, Foggia, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- al-Farabi Kazakh National University, Almaty, Kazakhstan
- * E-mail:
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