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Zhang X, Yang M, Liu Z, Yang F, Zhang L, Guo Y, Huo D. Genetic analysis of yield components in buckwheat using high-throughput sequencing analysis and wild resource populations. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1313-1328. [PMID: 39184561 PMCID: PMC11341512 DOI: 10.1007/s12298-024-01491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/06/2024] [Accepted: 07/15/2024] [Indexed: 08/27/2024]
Abstract
Fagopyrum tataricum, an important medicinal and edible crop, possesses significant agricultural and economic value. However, the development of buckwheat varieties and yields has been hindered by the delayed breeding progress despite the abundant material resources in China. Current research indicates that quantitative trait loci (QTLs) play a crucial role in controlling plant seed type and yield. To address these limitations, this study constructed recombinant inbred lines (RILs) utilizing both cultivated species and wild buckwheat as raw materials. In total, 84,521 Single Nucleotide Polymorphism (SNP) markers were identified through Genotyping-by-Sequencing (GBS) technology, and high-resolution and high-density SNP genetic maps were developed, which had significant value for QTL mapping, gene cloning and comparative mapping of buckwheat. In this study, we successfully identified 5 QTLs related to thousand grain weight (TGW), 9 for grain length (GL), and 1 for grain width (GW) by combining seed type and TGW data from 202 RIL populations in four different environments, within which one co-located QTL for TGW were discovered on the first chromosome. Transcriptome analysis during different grain development stages revealed 59 significant expression differences between the two materials, which can serve as candidate genes for further investigation into the regulation of grain weight and yield enhancement. The mapped major loci controlling TGW, GL and GW will be valuable for gene cloning and reveal the mechanism underlying grain development and marker-assisted selection in Tartary buckwheat.
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Affiliation(s)
- Xiao Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Miao Yang
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031 China
| | - Fan Yang
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Lei Zhang
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Yajing Guo
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
| | - Dongao Huo
- College of Biological Sciences and Technology, Taiyuan Normal University, Jinzhong, 030619 China
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Guden B, Yol E, Erdurmus C, Lucas SJ, Uzun B. Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [ Sorghum bicolor (L.) Moench]. FRONTIERS IN PLANT SCIENCE 2023; 14:1081931. [PMID: 37342135 PMCID: PMC10278949 DOI: 10.3389/fpls.2023.1081931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/15/2023] [Indexed: 06/22/2023]
Abstract
Sorghum is an important but arguably undervalued cereal crop, grown in large areas in Asia and Africa due to its natural resilience to drought and heat. There is growing demand for sweet sorghum as a source of bioethanol as well as food and feed. The improvement of bioenergy-related traits directly affects bioethanol production from sweet sorghum; therefore, understanding the genetic basis of these traits would enable new cultivars to be developed for bioenergy production. In order to reveal the genetic architecture behind bioenergy-related traits, we generated an F2 population from a cross between sweet sorghum cv. 'Erdurmus' and grain sorghum cv. 'Ogretmenoglu'. This was used to construct a genetic map from SNPs discovered by double-digest restriction-site associated DNA sequencing (ddRAD-seq). F3 lines derived from each F2 individual were phenotyped for bioenergy-related traits in two different locations and their genotypes were analyzed with the SNPs to identify QTL regions. On chromosomes 1, 7, and 9, three major plant height (PH) QTLs (qPH1.1, qPH7.1, and qPH9.1) were identified, with phenotypic variation explained (PVE) ranging from 10.8 to 34.8%. One major QTL (qPJ6.1) on chromosome 6 was associated with the plant juice trait (PJ) and explained 35.2% of its phenotypic variation. For fresh biomass weight (FBW), four major QTLs (qFBW1.1, qFBW6.1, qFBW7.1, and qFBW9.1) were determined on chromosomes 1, 6, 7, and 9, which explained 12.3, 14.5, 10.6, and 11.9% of the phenotypic variation, respectively. Moreover, two minor QTLs (qBX3.1 and qBX7.1) of Brix (BX) were mapped on chromosomes 3 and 7, explaining 8.6 and 9.7% of the phenotypic variation, respectively. The QTLs in two clusters (qPH7.1/qBX7.1 and qPH7.1/qFBW7.1) overlapped for PH, FBW and BX. The QTL, qFBW6.1, has not been previously reported. In addition, eight SNPs were converted into cleaved amplified polymorphic sequences (CAPS) markers, which can be easily detected by agarose gel electrophoresis. These QTLs and molecular markers can be used for pyramiding and marker-assisted selection studies in sorghum, to develop advanced lines that include desirable bioenergy-related traits.
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Affiliation(s)
- Birgul Guden
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Cengiz Erdurmus
- Department of Field Crops, West Mediterranean Agricultural Research Institute, Antalya, Türkiye
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Centre, Sabanci University, Istanbul, Türkiye
| | - Bulent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
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Ye M, Wan H, Yang W, Liu Z, Wang Q, Yang N, Long H, Deng G, Yang Y, Feng H, Zhou Y, Yang C, Li J, Zhang H. Precisely mapping a major QTL for grain weight on chromosome 5B of the founder parent Chuanmai42 in the wheat-growing region of southwestern China. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:146. [PMID: 37258797 DOI: 10.1007/s00122-023-04383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
KEY MESSAGE QTgw.saas-5B was validated as a major thousand-grain weight-related QTL in a founder parent used for wheat breeding and then precisely mapped to a 0.6 cM interval. Increasing the thousand-grain weight (TGW) is considered to be one of the most important ways to improve yield, which is a core objective among wheat breeders. Chuanmai42, which is a wheat cultivar with high TGW and a high and stable yield, is a parent of more than 30 new varieties grown in southwestern China. In this study, a Chuanmai42-derived recombinant inbred line (RIL) population was used to dissect the genetic basis of TGW. A major QTL (QTgw.saas-5B) mapped to the Xgwm213-Xgwm540 interval on chromosome 5B of Chuanmai42 explained up to 20% of the phenotypic variation. Using 71 recombinants with a recombination in the QTgw.saas-5B interval identified from a secondary RIL population comprising 1818 lines constructed by crossing the QTgw.saas-5B near-isogenic line with the recurrent parent Chuannong16, QTgw.saas-5B was delimited to a 0.6 cM interval, corresponding to a 21.83 Mb physical interval in the Chinese Spring genome. These findings provide the foundation for QTgw.saas-5B cloning and its use in molecular marker-assisted breeding.
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Affiliation(s)
- Meijin Ye
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
| | - Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Ning Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yumin Yang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Hong Feng
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cairong Yang
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China.
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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Adel S, Carels N. Plant Tolerance to Drought Stress with Emphasis on Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112170. [PMID: 37299149 DOI: 10.3390/plants12112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 06/12/2023]
Abstract
Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.
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Affiliation(s)
- Sarah Adel
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development for Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-361, Brazil
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5
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Wan H, Yang M, Li J, Wang Q, Liu Z, Zheng J, Li S, Yang N, Yang W. Cytological and genetic effects of rye chromosomes 1RS and 3R on the wheat-breeding founder parent Chuanmai 42 from southwestern China. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:40. [PMID: 37312750 PMCID: PMC10248656 DOI: 10.1007/s11032-023-01386-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/13/2023] [Indexed: 06/15/2023]
Abstract
Rye (Secale cereale L.) is an important genetic resource for improving the disease resistance of wheat. An increasing number of rye chromosome segments have been transferred into modern wheat cultivars via chromatin insertions. In this study, 185 recombinant inbred lines (RILs) derived from a cross between a wheat accession containing rye chromosomes 1RS and 3R and a wheat-breeding founder parent Chuanmai 42 from southwestern China were used to decipher the cytological and genetic effects of 1RS and 3R via fluorescence/genomic in situ hybridization and quantitative trait locus (QTL) analyses. Chromosome centromere breakage and fusion were detected in the RIL population. Additionally, the recombination of chromosomes 1BS and 3D from Chuanmai 42 was completely suppressed by 1RS and 3R in the RIL population. In contrast to chromosome 3D of Chuanmai 42, rye chromosome 3R was significantly associated with white seed coats and decreased yield-related traits, as revealed by QTL and single marker analyses, whereas it had no effect on stripe rust resistance. Rye chromosome 1RS did not affect yield-related traits and it increased the susceptibility of plants to stripe rust. Most of the detected QTLs that positively affected yield-related traits were from Chuanmai 42. The findings of this study suggest that the negative effects of rye-wheat substitutions or translocations, including the suppression of the pyramiding of favorable QTLs on paired wheat chromosomes from different parents and the transfer of disadvantageous alleles to filial generations, should be considered when selecting alien germplasm to enhance wheat-breeding founder parents or to breed new varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01386-0.
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Affiliation(s)
- Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Manyu Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Jianmin Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Shizhao Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Ning Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066 China
- Key Laboratory of Wheat Biology and Genetic Improvement On Southwestern China (MARA), Chengdu, 610066 China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
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Zhao J, Sun L, Gao H, Hu M, Mu L, Cheng X, Wang J, Zhao Y, Li Q, Wang P, Li H, Zhang Y. Genome-wide association study of yield-related traits in common wheat ( Triticum aestivum L.) under normal and drought treatment conditions. FRONTIERS IN PLANT SCIENCE 2023; 13:1098560. [PMID: 36684753 PMCID: PMC9846334 DOI: 10.3389/fpls.2022.1098560] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The primary goal of modern wheat breeding is to develop new high-yielding and widely adaptable varieties. We analyzed four yield-related agronomic traits in 502 wheat accessions under normal conditions (NC) and drought treatment (DT) conditions over three years. The genome-wide association analysis identified 51 yield-related and nine drought-resistance-related QTL, including 13 for the thousand-grain weight (TGW), 30 for grain length (GL), three for grain width (GW), five for spike length (SL) and nine for stress tolerance index (STI) QTL in wheat. These QTL, containing 72 single nucleotide polymorphisms (SNPs), explained 2.23 - 7.35% of the phenotypic variation across multiple environments. Eight stable SNPs on chromosomes 2A, 2D, 3B, 4A, 5B, 5D, and 7D were associated with phenotypic stability under NC and DT conditions. Two of these stable SNPs had association with TGW and STI. Several novel QTL for TGW, GL and SL were identified on different chromosomes. Three linked SNPs were transformed into kompetitive allele-specific PCR (KASP) markers. These results will facilitate the discovery of promising SNPs for yield-related traits and/or drought stress tolerance and will accelerate the development of new wheat varieties with desirable alleles.
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Affiliation(s)
- Jie Zhao
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Lijing Sun
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Huimin Gao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Mengyun Hu
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Liming Mu
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Xiaohu Cheng
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Jianbing Wang
- Institute of Cereal Crops, Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Yun Zhao
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Qianying Li
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Peinan Wang
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Hui Li
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yingjun Zhang
- Institute of Cereal and Oil Crops, Laboratory of Crop Genetics and Breeding of Hebei, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
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Vervalle JA, Costantini L, Lorenzi S, Pindo M, Mora R, Bolognesi G, Marini M, Lashbrooke JG, Tobutt KR, Vivier MA, Roodt-Wilding R, Grando MS, Bellin D. A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4371-4390. [PMID: 36271055 PMCID: PMC9734222 DOI: 10.1007/s00122-022-04225-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
We present a high-density integrated map for grapevine, allowing refinement and improved understanding of the grapevine genome, while demonstrating the applicability of the Vitis18K SNP chip for linkage mapping. The improvement of grapevine through biotechnology requires identification of the molecular bases of target traits by studying marker-trait associations. The Vitis18K SNP chip provides a useful genotyping tool for genome-wide marker analysis. Most linkage maps are based on single mapping populations, but an integrated map can increase marker density and show order conservation. Here we present an integrated map based on three mapping populations. The parents consist of the well-known wine cultivars 'Cabernet Sauvignon', 'Corvina' and 'Rhine Riesling', the lesser-known wine variety 'Deckrot', and a table grape selection, G1-7720. Three high-density population maps with an average inter-locus gap ranging from 0.74 to 0.99 cM were developed. These maps show high correlations (0.9965-0.9971) with the reference assembly, containing only 93 markers with large order discrepancies compared to expected physical positions, of which a third is consistent across multiple populations. Moreover, the genetic data aid the further refinement of the grapevine genome assembly, by anchoring 104 yet unanchored scaffolds. From these population maps, an integrated map was constructed which includes 6697 molecular markers and reduces the inter-locus gap distance to 0.60 cM, resulting in the densest integrated map for grapevine thus far. A small number of discrepancies, mainly of short distance, involve 88 markers that remain conflictual across maps. The integrated map shows similar collinearity to the reference assembly (0.9974) as the single maps. This high-density map increases our understanding of the grapevine genome and provides a useful tool for its further characterization and the dissection of complex traits.
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Affiliation(s)
- Jessica A Vervalle
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
- ARC Infruitec-Nietvoorbij, Stellenbosch, 7599, South Africa
| | - Laura Costantini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Silvia Lorenzi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Riccardo Mora
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Giada Bolognesi
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Martina Marini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Justin G Lashbrooke
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Ken R Tobutt
- ARC Infruitec-Nietvoorbij, Stellenbosch, 7599, South Africa
| | - Melané A Vivier
- South African Grape and Wine Research Institute, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Maria Stella Grando
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Center Agriculture Food and Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy.
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8
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High-Density Linkage Mapping of Agronomic Trait QTLs in Wheat under Water Deficit Condition using Genotyping by Sequencing (GBS). PLANTS 2022; 11:plants11192533. [PMID: 36235399 PMCID: PMC9571144 DOI: 10.3390/plants11192533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022]
Abstract
Improvement of grain yield is the ultimate goal for wheat breeding under water-limited environments. In the present study, a high-density linkage map was developed by using genotyping-by-sequencing (GBS) of a recombinant inbred line (RIL) population derived from the cross between Iranian landrace #49 and cultivar Yecora Rojo. The population was evaluated in three locations in Iran during two years under irrigated and water deficit conditions for the agronomic traits grain yield (GY), plant height (PH), spike number per square meter (SM), 1000 kernel weight (TKW), grain number per spike (GNS), spike length (SL), biomass (BIO) and harvest index (HI). A linkage map was constructed using 5831 SNPs assigned to 21 chromosomes, spanning 3642.14 cM of the hexaploid wheat genome with an average marker density of 0.62 (markers/cM). In total, 85 QTLs were identified on 19 chromosomes (all except 5D and 6D) explaining 6.06–19.25% of the traits phenotypic variance. We could identify 20 novel QTLs explaining 8.87–19.18% of phenotypic variance on chromosomes 1A, 1B, 1D, 2B, 3A, 3B, 6A, 6B and 7A. For 35 out of 85 mapped QTLs functionally annotated genes were identified which could be related to a potential role in drought stress.
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9
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Niu Y, Chen T, Zhao C, Guo C, Zhou M. Identification of QTL for Stem Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:962253. [PMID: 35909739 PMCID: PMC9330363 DOI: 10.3389/fpls.2022.962253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Lodging in wheat (Triticum aestivum L.) is a complicated phenomenon that is influenced by physiological, genetics, and external factors. It causes a great yield loss and reduces grain quality and mechanical harvesting efficiency. Lodging resistance is contributed by various traits, including increased stem strength. The aim of this study was to map quantitative trait loci (QTL) controlling stem strength-related features (the number of big vascular bundles, stem diameter, stem wall thickness) using a doubled haploid (DH) population derived from a cross between Baiqimai and Neixiang 5. Field experiments were conducted during 2020-2022, and glasshouse experiments were conducted during 2021-2022. Significant genetic variations were observed for all measured traits, and they were all highly heritable. Fifteen QTL for stem strength-related traits were identified on chromosomes 2D, 3A, 3B, 3D, 4B, 5A, 6B, 7A, and 7D, respectively, and 7 QTL for grain yield-related traits were identified on chromosomes 2B, 2D, 3D, 4B, 7A, and 7B, respectively. The superior allele of the major QTL for the number of big vascular bundle (VB) was independent of plant height (PH), making it possible to improve stem strength without a trade-off of PH, thus improving lodging resistance. VB also showed positive correlations with some of the yield components. The result will be useful for molecular marker-assisted selection (MAS) for high stem strength and high yield potential.
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Affiliation(s)
- Yanan Niu
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Tianxiao Chen
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ce Guo
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- College of Agronomy, Shanxi Agricultural University, Taigu, China
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