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Plotnikov KO, Klimenko AI, Ovchinnikova ES, Lashin SA, Goncharov NP. Analysis of the Effects of the Vrn-1 and Ppd-1 Alleles on Adaptive and Agronomic Traits in Common Wheat ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1453. [PMID: 38891261 PMCID: PMC11174496 DOI: 10.3390/plants13111453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Wheat heading time is primarily governed by two loci: VRN-1 (response to vernalization) and PPD-1 (response to photoperiod). Five sets of near-isogenic lines (NILs) were studied with the aim of investigating the effect of the aforementioned genes on wheat vegetative period duration and 14 yield-related traits. Every NIL was sown in the hydroponic greenhouse of the Institute of Cytology and Genetics, SB RAS. To assess their allelic composition at the VRN-1 and PPD-1 loci, molecular markers were used. It was shown that HT in plants with the Vrn-A1vrn-B1vrn-D1 genotype was reduced by 29 and 21 days (p < 0.001) in comparison to HT in plants with the vrn-A1Vrn-B1vrn-D1 and the vrn-A1vrn-B1Vrn-D1 genotypes, respectively. In our study, we noticed a decrease in spike length as well as spikelet number per spike parameter for some NIL carriers of the Vrn-A1a allele in comparison to carriers of the Vrn-B1 allele. PCA revealed three first principal components (PC), together explaining more than 70% of the data variance. Among the studied genetic traits, the Vrn-A1a and Ppd-D1a alleles showed significant correlations with PCs. Regarding genetic components, significant correlations were calculated between PC3 and Ppd-B1a (-0.26, p < 0.05) and Vrn-B1 (0.57, p < 0.05) alleles. Thus, the presence of the Vrn-A1a allele affects heading time, while Ppd-D1a is associated with plant height reduction.
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Affiliation(s)
- Kirill O. Plotnikov
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia
| | - Alexandra I. Klimenko
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia (S.A.L.)
| | - Ekaterina S. Ovchinnikova
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia
| | - Sergey A. Lashin
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia (S.A.L.)
| | - Nikolay P. Goncharov
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia
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Xu H, Wang Z, Wang F, Hu X, Ma C, Jiang H, Xie C, Gao Y, Ding G, Zhao C, Qin R, Cui D, Sun H, Cui F, Wu Y. Genome-wide association study and genomic selection of spike-related traits in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:131. [PMID: 38748046 DOI: 10.1007/s00122-024-04640-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/27/2024] [Indexed: 06/09/2024]
Abstract
KEY MESSAGE Identification of 337 stable MTAs for wheat spike-related traits improved model accuracy, and favorable alleles of MTA259 and MTA64 increased grain weight and yield per plant. Wheat (Triticum aestivum L.) is one of the three primary global, staple crops. Improving spike-related traits in wheat is crucial for optimizing spike and plant morphology, ultimately leading to increased grain yield. Here, we performed a genome-wide association study using a dataset of 24,889 high-quality unique single-nucleotide polymorphisms (SNPs) and phenotypic data from 314 wheat accessions across eight diverse environments. In total, 337 stable and significant marker-trait associations (MTAs) related to spike-related traits were identified. MTA259 and MTA64 were consistently detected in seven and six environments, respectively. The presence of favorable alleles associated with MTA259 and MTA64 significantly reduced wheat spike exsertion length and spike length, while enhancing thousand kernel weight and yield per plant. Combined gene expression and network analyses identified TraesCS6D03G0692300 and TraesCS6D03G0692700 as candidate genes for MTA259 and TraesCS2D03G0111700 and TraesCS2D03G0112500 for MTA64. The identified MTAs significantly improved the prediction accuracy of each model compared with using all the SNPs, and the random forest model was optimal for genome selection. Additionally, the eight stable and major MTAs, including MTA259, MTA64, MTA66, MTA94, MTA110, MTA165, MTA180, and MTA164, were converted into cost-effective and efficient detection markers. This study provided valuable genetic resources and reliable molecular markers for wheat breeding programs.
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Affiliation(s)
- Huiyuan Xu
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Zixu Wang
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Faxiang Wang
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Xinrong Hu
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Chengxue Ma
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Huijiao Jiang
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Chang Xie
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Yuhang Gao
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Guangshuo Ding
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Chunhua Zhao
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Ran Qin
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Dezhou Cui
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Key Laboratory of Wheat Biology and Genetics and Breeding in Northern Huang-Huai River Plain, Ministry of Agriculture and Rural Affairs/Shandong Technology Innovation Center of Wheat/Jinan Key Laboratory of Wheat Genetic Improvement, Jinan, Shandong, China
| | - Han Sun
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China.
| | - Fa Cui
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China.
| | - Yongzhen Wu
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China.
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Si Y, Tian S, Niu J, Yu Z, Ma S, Lu Q, Wu H, Ling HQ, Zheng S. Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:240. [PMID: 37930446 DOI: 10.1007/s00122-023-04488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE Five environmentally stable QTLs for spikelet number per spike and days to heading were identified using a high-genetic map containing 95,444 SNPs, among which QSns.ucas-5B was validated using residual heterozygous line at multiple environments. Spikelet number per spike (SNS) and days to heading (DTH) play pivotal roles in the improvement of wheat yield. In this study, a high-density genetic map for a recombinant inbred lines (RILs) population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) was constructed using 95,444 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Our study identified a total of five environmentally stable QTLs for SNS and DTH, one of which was named QSns.ucas-5B, with a physical interval of approximately 545.4-552.1 Mb on the 5BL chromosome arm. Importantly, the elite haplotype within QSns.ucas-5B showed a consistent and positive effect on SNS, grain number and weight per spike, without extending the days to heading. These findings provide a foundation for future efforts to map and clone the gene(s) responsible for QSns.ucas-5B and further indicate the potential application of the developed and validated InDel marker of QSns.ucas-5B for molecular breeding purposes, aimed at improving wheat grain yield.
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Affiliation(s)
- Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqing Niu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongqing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Shengwei Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ahmed SF, Ahmed JU, Hasan M, Mohi-Ud-Din M. Assessment of genetic variation among wheat genotypes for drought tolerance utilizing microsatellite markers and morpho-physiological characteristics. Heliyon 2023; 9:e21629. [PMID: 38027610 PMCID: PMC10658252 DOI: 10.1016/j.heliyon.2023.e21629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/18/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Drought is a major abiotic stress that severely limits sustainable wheat (Triticum aestivum L.) productivity via morphological and physio-biochemical alterations of cellular processes. The complex nature and polygenic control of drought tolerance traits make breeding tolerant genotypes quite challenging. However, naturally occurring variabilities among wheat germplasm resources could potentially help combating drought. The present study was conducted to assess the drought tolerance of 18 Bangladeshi hexaploid wheat genotypes, focusing on the identification of potent sources of diversity by combining microsatellite markers, also known as single sequence repeat markers, and morpho-physiological characteristics that might help accelerating wheat crop improvement programs. Initially, the genotypes were evaluated using 25 microsatellite markers followed by an on-field evaluation of 7 morphological traits (plant height, spike number, spike length, grains per spike, 1000-grain weight, grain yield, biological yield) and 6 physiological traits (SPAD value, membrane stability index, leaf relative water content, proline content, canopy temperature depression, and leaf K+ ion content). The field-trial was conducted in a factorial fashion of 18 wheat genotypes and two water regimes (control and drought) following a split-plot randomized complete block design. Regardless of genotype, drought was significantly damaging for all the tested traits; however, substantial variability in drought stress tolerance was evident among the genotypes. Spike length, 1000-grain weight, SPAD value, leaf relative water content, canopy temperature depression, proline content, and potassium (K+) ion content were the most representative of drought-induced growth and yield impairments and also correlated well with the contrasting ability of genotypic tolerance. Microsatellite markers amplified 244 alleles exhibiting 79% genetic diversity. Out of 25 markers, 23 was highly polymorphic showing 77% average polymorphism. Morpho-physiological trait-based hierarchical clustering and microsatellite marker-based neighbor-jointing clustering both revealed three genotypic clusters with 71% co-linearity between them. In both cases, the genotypes Kanchan, BAW-1147, BINA Gom 1, BARI Gom 22, BARI Gom 26, and BARI Gom 33 were found to be comparatively more tolerant than the other tested genotypes, showing potential for cultivation in water-deficit environments. The findings of this study would contribute to the present understanding of drought tolerance in wheat and would provide a basis for future genotype selection for drought-tolerant wheat breeding programs.
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Affiliation(s)
- Sheikh Faruk Ahmed
- Department of Crop Botany, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Jalal Uddin Ahmed
- Department of Crop Botany, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Mehfuz Hasan
- Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
| | - Mohammed Mohi-Ud-Din
- Department of Crop Botany, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh
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5
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Dallinger HG, Löschenberger F, Bistrich H, Ametz C, Hetzendorfer H, Morales L, Michel S, Buerstmayr H. Predictor bias in genomic and phenomic selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:235. [PMID: 37878079 PMCID: PMC10600307 DOI: 10.1007/s00122-023-04479-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/08/2023] [Indexed: 10/26/2023]
Abstract
KEY MESSAGE NIRS of wheat grains as phenomic predictors for grain yield show inflated prediction ability and are biased toward grain protein content. Estimating the breeding value of individuals using genome-wide marker data (genomic prediction) is currently one of the most important drivers of breeding progress in major crops. Recently, phenomic technologies, including remote sensing and aerial hyperspectral imaging of plant canopies, have made it feasible to predict the breeding value of individuals in the absence of genetic marker data. This is commonly referred to as phenomic prediction. Hyperspectral measurements in the form of near-infrared spectroscopy have been used since the 1980 s to predict compositional parameters of harvest products. Moreover, in recent studies NIRS from grains was used to predict grain yield. The same studies showed that phenomic prediction can outperform genomic prediction for grain yield. The genome is static and not environment dependent, thereby limiting genomic prediction ability. Gene expression is tissue specific and differs under environmental influences, leading to a tissue- and environment-specific phenome, potentially explaining the higher predictive ability of phenomic prediction. Here, we compare genomic prediction and phenomic prediction from hyperspectral measurements of wheat grains for the prediction of a variety of traits including grain yield. We show that phenomic predictions outperform genomic prediction for some traits. However, phenomic predictions are biased toward the information present in the predictor. Future studies on this topic should investigate whether population parameters are retained in phenomic prediction as they are in genomic prediction. Furthermore, we find that unbiased phenomic prediction abilities are considerably lower than previously reported and recommend a method to circumvent this issue.
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Affiliation(s)
- Hermann Gregor Dallinger
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
- Saatzucht Donau GesmbH & Co KG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria.
| | | | - Herbert Bistrich
- Saatzucht Donau GesmbH & Co KG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Christian Ametz
- Saatzucht Donau GesmbH & Co KG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | | | - Laura Morales
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Sebastian Michel
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
| | - Hermann Buerstmayr
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
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6
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Yang X, Cai L, Wang M, Zhu W, Xu L, Wang Y, Zeng J, Fan X, Sha L, Wu D, Cheng Y, Zhang H, Jiang Y, Chen G, Zhou Y, Kang H. Genome-Wide Association Study of Asian and European Common Wheat Accessions for Yield-Related Traits and Stripe Rust Resistance. PLANT DISEASE 2023; 107:3085-3095. [PMID: 37079013 DOI: 10.1094/pdis-03-22-0702-re] [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: 05/03/2023]
Abstract
Identifying novel loci of yield-related traits and resistance to stripe rust (caused by Puccinia striiformis f. sp. tritici) in wheat will help in breeding wheat that can meet projected demands in diverse environmental and agricultural practices. We performed a genome-wide association study with 24,767 single nucleotide polymorphisms (SNPs) in 180 wheat accessions that originated in 16 Asian or European countries between latitudes 30°N and 45°N. We detected seven accessions with desirable yield-related traits and 42 accessions that showed stable, high degrees of stripe rust resistance in multienvironment field assessments. A marker-trait association analysis of yield-related traits detected 18 quantitative trait loci (QTLs) in at least two test environments and two QTLs related to stripe rust resistance in at least three test environments. Five of these QTLs were identified as potentially novel QTLs by comparing their physical locations with those of known QTLs in the Chinese Spring (CS) reference genome RefSeq v1.1 published by the International Wheat Genome Sequencing Consortium; two were for spike length, one was for grain number per spike, one was for spike number, and one was for stripe rust resistance at the adult plant stage. We also identified 14 candidate genes associated with the five novel QTLs. These QTLs and candidate genes will provide breeders with new germplasm and can be used to conduct marker-assisted selection in breeding wheat with improved yield and stripe rust resistance.
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Affiliation(s)
- Xiu Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Li Cai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Miaomiao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Lili Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Lina Sha
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Haiqin Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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7
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Golan G, Abbai R, Schnurbusch T. Exploring the trade-off between individual fitness and community performance of wheat crops using simulated canopy shade. PLANT, CELL & ENVIRONMENT 2023; 46:3144-3157. [PMID: 36428231 DOI: 10.1111/pce.14499] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
The genetic heritage of wheat (Triticum spp.) crops has been shaped by millions of years of predomestication natural selection, often driven by competition among individuals. However, genetic improvements in yield potential are thought to involve selection towards reduced competitiveness, thus enhancing adaptation to the crop environment. We investigated potential trade-offs between individual plant fitness and community performance using a population of introgression lines carrying chromosome segments of wild emmer (nondomesticated) in the background of an elite durum cultivar. We focused on light as a primary factor affecting plant-plant interactions and assessed morphological and biomass phenotypes of single plants grown in mixtures under sunlight and a simulated canopy shade, and the relevance of these phenotypes for the monoculture community in the field. We found that responses to canopy shade resemble responses to high density and contribute to both the individual and the community. Stepwise regressions suggested that grain number per spike and its persistence under shade are essential attributes of productive communities, advocating their use as a breeding target during early-generation selection. Overall, multiple phenotypes attained under shade could better explain community performance. Our novel, applicable, high-throughput set-up provides new prospects for studying and selecting single-plant phenotypes in a canopy-like environment.
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Affiliation(s)
- Guy Golan
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
| | - Ragavendran Abbai
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
| | - Thorsten Schnurbusch
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
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8
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Li Z, Luo Q, Deng Y, Du K, Li X, Ren T. Identification and Validation of a Stable Major-Effect Quantitative Trait Locus for Kernel Number per Spike on Chromosome 2D in Wheat ( Triticum aestivum L.). Int J Mol Sci 2023; 24:14289. [PMID: 37762591 PMCID: PMC10531874 DOI: 10.3390/ijms241814289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
A recombinant inbred line population including 371 lines was developed by a high kernel number per spike (KNPS) genotype T1208 and a low KNPS genotype Chuannong18 (CN18). A genetic linkage map consisting of 11,583 markers was constructed by the Wheat55K SNP Array. The quantitative trait loci (QTLs) related to KNPS were detected in three years. Eight, twenty-seven, and four QTLs were identified using the ICIM-BIP, ICIM-MET, and ICIM-EPI methods, respectively. One QTL, QKnps.sau-2D.1, which was mapped on chromosome 2D, can explain 18.10% of the phenotypic variation (PVE) on average and be considered a major and stable QTL for KNPS. This QTL was located in a 0.89 Mb interval on chromosome 2D and flanked by the markers AX-109283238 and AX-111606890. Moreover, KASP-AX-111462389, a Kompetitive Allele-Specific PCR (KASP) marker which closely linked to QKnps.sau-2D.1, was designed. The genetic effect of QKnps.sau-2D.1 on KNPS was successfully confirmed in two RIL populations. The results also showed that the significant increase of KNPS and 1000-kernel weight (TKW) was caused by QKnps.sau-2D.1 overcoming the disadvantage due to the decrease of spike number (SN) and finally lead to a significant increase of grain yield. In addition, within the interval in which QKnps.sau-2D.1 is located in Chinese Spring reference genomes, only fifteen genes were found, and two genes that might associate with KNPS were identified. QKnps.sau-2D.1 may provide a new resource for the high-yield breeding of wheat in the future.
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Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China;
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Qinyi Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Yawen Deng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Ke Du
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Xinli Li
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Tianheng Ren
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China;
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
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9
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Backhaus AE, Griffiths C, Vergara-Cruces A, Simmonds J, Lee R, Morris RJ, Uauy C. Delayed development of basal spikelets in wheat explains their increased floret abortion and rudimentary nature. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5088-5103. [PMID: 37338600 PMCID: PMC10498016 DOI: 10.1093/jxb/erad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/15/2023] [Indexed: 06/21/2023]
Abstract
Large differences exist in the number of grains per spikelet across an individual wheat (Triticum aestivum L.) spike. The central spikelets produce the highest number of grains, while apical and basal spikelets are less productive, and the most basal spikelets are commonly only developed in rudimentary form. Basal spikelets are delayed in initiation, yet they continue to develop and produce florets. The precise timing or the cause of their abortion remains largely unknown. Here, we investigated the underlying causes of basal spikelet abortion using shading applications in the field. We found that basal spikelet abortion is likely to be the consequence of complete floret abortion, as both occur concurrently and have the same response to shading treatments. We detected no differences in assimilate availability across the spike. Instead, we show that the reduced developmental age of basal florets pre-anthesis is strongly associated with their increased abortion. Using the developmental age pre-abortion, we were able to predict final grain set per spikelet across the spike, alongside the characteristic gradient in the number of grains from basal to central spikelets. Future efforts to improve spikelet homogeneity across the spike could thus focus on improving basal spikelet establishment and increasing floret development rates pre-abortion.
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Affiliation(s)
| | - Cara Griffiths
- Plant Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | | | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Rebecca Lee
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Richard J Morris
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
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10
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Liu Y, Chen J, Yin C, Wang Z, Wu H, Shen K, Zhang Z, Kang L, Xu S, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Gong Y, Yu X, Sun Z, Ye B, Liu D, Zhang L, Shen L, Hao Y, Ma Y, Lu F, Guo Z. A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat. Genome Biol 2023; 24:196. [PMID: 37641093 PMCID: PMC10463835 DOI: 10.1186/s13059-023-03044-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments. RESULTS We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection. CONCLUSION Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Lipeng Kang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Song Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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11
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Zhang Y, Miao H, Xiao Y, Wang C, Zhang J, Shi X, Xie S, Wang C, Li T, Deng P, Chen C, Zhang H, Ji W. An intron-located single nucleotide variation of TaGS5-3D is related to wheat grain size through accumulating intron retention transcripts. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:193. [PMID: 37606787 DOI: 10.1007/s00122-023-04439-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE Thirty-three stable QTL for 13 yield-related traits across ten environments were identified in the PD34/MY47 RIL population, and a candidate gene TaGS5-3D in Qmt.nwafu.3D was preliminarily identified to affect grain-related traits through accumulation of specific transcripts. Dissecting the genetic basis of yield-related traits is pivotal for improvement of wheat yield potential. In this study, a recombinant inbred line (RIL) population genotyped by SNP markers was used to detect quantitative trait loci (QTL) related to yield-related traits in ten environments. A total of 102 QTL were detected, including 33 environmentally stable QTL and 69 putative QTL. Among them, Qmt.nwafu.3D was identified as a pleiotropic QTL in the physical interval of 149.77-154.11 Mb containing a potential candidate gene TaGS5-3D. An SNP (T > C) was detected in its ninth intron, and TaGS5-3D-C was validated as a superior allele associated with larger grains using a CAPS marker. Interestingly, we found that TaGS5-3D-C was closely related to significantly up-regulated expression of intron-retained transcript (TaGS5-3D-PD34.1), while TaGS5-3D-T was related to dominant expression of normal splicing transcript (TaGS5-3D-MY47.1). Our results indicated that alternative splicing associated with the SNP T/C could be involved in the regulation of grain-related traits, laying a foundation for the functional analysis of TaGS5-3D and its greater potential application in high-yield wheat breeding.
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Affiliation(s)
- Yaoyuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Hanxiao Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yi Xiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Junjie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaoxi Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Songfeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China.
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12
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Wang Y, Zeng Z, Li J, Zhao D, Zhao Y, Peng C, Lan C, Wang C. Identification and validation of new quantitative trait loci for spike-related traits in two RIL populations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:64. [PMID: 37533603 PMCID: PMC10390419 DOI: 10.1007/s11032-023-01401-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important cereal crops for ensuring food security worldwide. Identification of major quantitative trait loci (QTL) for spike-related traits is important for improvement of yield potential in wheat breeding. In this study, by using the wheat 55K single nucleotide polymorphism (SNP) array and diversity array technology (DArT), two recombinant inbred line populations derived from crosses avocet/chilero and avocet/huites were used to map QTL for kernel number per spike (KNS), total spikelet number per spike (TSS), fertile spikelet number per spike (FSS), and spike compactness (SC). Forty-two QTLs were identified on chromosomes 2A (4), 2B (3), 3A (2), 3B (7), 5A (11), 6A (4), 6B, and 7A (10), explaining 3.13-21.80% of the phenotypic variances. Twelve QTLs were detected in multi-environments on chromosomes 2A, 3B (2), 5A (4), 6A (3), 6B, and 7A, while four QTL clusters were detected on chromosomes 3A, 3B, 5A, and 7A. Two stable and new QTL clusters, QKns/Tss/Fss/SC.haust-5A and QKns/Tss/Fss.haust-7A, were detected in the physical intervals of 547.49-590.46 Mb and 511.54-516.15 Mb, accounting for 7.53-14.78% and 7.01-20.66% of the phenotypic variances, respectively. High-confidence annotated genes for QKns/Tss/Fss/SC.haust-5A and QKns/Tss/Fss.haust-7A were more highly expressed in spike development. The results provide new QTL and molecular markers for marker-assisted breeding in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01401-4.
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Affiliation(s)
- Yuying Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Zhankui Zeng
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Jiachuang Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Dehui Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Yue Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Chen Peng
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, 471000 Henan China
- The Shennong Laboratory, Zhengzhou, 450002 Henan China
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13
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Al-Sayaydeh R, Shtaya MJ, Qubbaj T, Al-Rifaee MK, Alabdallah MA, Migdadi O, Gammoh IA, Al-Abdallat AM. Performance and Stability Analysis of Selected Durum Wheat Genotypes Differing in Their Kernel Characteristics. PLANTS (BASEL, SWITZERLAND) 2023; 12:2664. [PMID: 37514278 PMCID: PMC10384256 DOI: 10.3390/plants12142664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023]
Abstract
Breeding of high-yielding and stable durum wheat varieties with improved kernel characteristics is needed for dry regions around the globe. The aim of this study was to investigate the performance and stability of eight durum wheat genotypes varying in their kernel characteristics across 15 contrasting environments. The tested material included three recombinant inbred lines (NUR-072, NUR-106 and NUR-238) derived from a cross between Norsi, a Jordanian landrace with special kernel characteristics and UC1113 Yr36+Gpc-B1, an elite line from USA. Field trials were carried out for three constitutive growing seasons under rainfed conditions, except for three environments where supplementary irrigation was provided. After the harvest, grain yield (GY), total yield (TW), and harvest index (HI) were recorded. Additionally, several kernel-related traits, including thousand kernel weight (TKW), kernel area (KA), kernel width (KW), kernel length (KL), kernel circularity (KC), and kernel length-width ratio (KL:KW) were evaluated. Analysis of variance for all tested traits revealed high significant variations (p ≤ 0.01) between the genotype (except for TW) and the genotype × environment (G × E) interaction. Genotype effect contributed to substantial percentage of variation (>75%) for KA, KL, KC and KL:KW, whereas KW showed a lower percentage similar to GY. Regarding the G × E effect, explained variation was highest for the TW (67.79%), and lowest for KL (6.47%). For GY, Norsi produced significantly the lowest mean value (249.99 g.m-2) while, Bolenga produced the highest mean value (377.85 g.m-2) although no significant differences were observed with the remaining genotypes. On the other hand, Norsi, NUR-072 and NUR-106 showed best performance for TKW and kernel-related traits with NUR-106 producing the highest mean value for KL (9.07 mm). The GGE biplot and AMMI analysis of GY identified Bolenga, Um Qais and NUR-106 as good performers across several environments, while Norsi exhibited the poorest performance. For TKW, Norsi was the best performer across different environments followed by NUR-106, which showed excellent performance under irrigated and saline conditions. For stability analysis, NUR-106 emerged as the most stable genotype in this study for GY and several kernel-related traits, particularly for KL and KC. In conclusion, the results of this study offer valuable insights for durum wheat breeders seeking to develop high-yielding and stable varieties with special kernel characteristics suitable for cultivation in dry areas.
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Affiliation(s)
- R Al-Sayaydeh
- Department of Agriculture Sciences, Faculty of Shoubak College, Al-Balqa Applied University, Al-Salt 19117, Jordan
| | - M J Shtaya
- Department of Plant Production and Protection, Faculty of Agriculture and Veterinary Medicine, An-Najah National University, Nablus P.O. Box 707, Palestine
| | - T Qubbaj
- Department of Plant Production and Protection, Faculty of Agriculture and Veterinary Medicine, An-Najah National University, Nablus P.O. Box 707, Palestine
| | - M K Al-Rifaee
- National Agricultural Research Center (NARC), Amman 19381, Jordan
| | - M A Alabdallah
- National Agricultural Research Center (NARC), Amman 19381, Jordan
| | - O Migdadi
- National Agricultural Research Center (NARC), Amman 19381, Jordan
| | - I A Gammoh
- Department of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman 11942, Jordan
| | - A M Al-Abdallat
- Department of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman 11942, Jordan
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14
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Taranto F, Esposito S, De Vita P. Genomics for Yield and Yield Components in Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2571. [PMID: 37447132 DOI: 10.3390/plants12132571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
In recent years, many efforts have been conducted to dissect the genetic basis of yield and yield components in durum wheat thanks to linkage mapping and genome-wide association studies. In this review, starting from the analysis of the genetic bases that regulate the expression of yield for developing new durum wheat varieties, we have highlighted how, currently, the reductionist approach, i.e., dissecting the yield into its individual components, does not seem capable of ensuring significant yield increases due to diminishing resources, land loss, and ongoing climate change. However, despite the identification of genes and/or chromosomal regions, controlling the grain yield in durum wheat is still a challenge, mainly due to the polyploidy level of this species. In the review, we underline that the next-generation sequencing (NGS) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms, as well as genome editing technology, will revolutionize plant breeding by providing a great opportunity to capture genetic variation that can be used in breeding programs. To date, genomic selection provides a valuable tool for modeling optimal allelic combinations across the whole genome that maximize the phenotypic potential of an individual under a given environment.
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Affiliation(s)
- Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 70126 Bari, Italy
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
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15
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Wang M, Lu J, Liu R, Li Y, Ao D, Wu Y, Zhang L. Identification and validation of a major quantitative trait locus for spike length and compactness in the wheat ( Triticum aestivum L.) line Chuanyu12D7. FRONTIERS IN PLANT SCIENCE 2023; 14:1186183. [PMID: 37469784 PMCID: PMC10353862 DOI: 10.3389/fpls.2023.1186183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
Spike length (SL) and spike compactness (SC) are crucial traits related to wheat (Triticum aestivum L.) yield potential. In this study, a backcrossed inbred lines (BILs) population segregating for SL/SC was developed by using a commercial variety chuanyu25 as recurrent parent and a backbone parent Chuanyu12D7. Bulked segregant analysis (BSA) combined with the Wheat 660K SNP array was performed to conduct quantitative trait locus (QTL) mapping. A major and stable SL/SC QTL (designated as QSl/Sc.cib-2D.1) was identified on chromosome 2DS, explaining 45.63-59.72% of the phenotypic variation. QSl/Sc.cib-2D.1 was mapped to a 102.29-Kb interval by flanking SNPs AX-110276364 and AX-111593853 using a BC4F2:3 population. Since QSl/Sc.cib-2D.1 is linked to the Rht8 gene, their additive effects on plant type and spike type were analysed. Remarkably, the superior allele of QSl/Sc.cib-2D.1 combined with Rht8 can increase SL and TGW, and decrese SC without any apparent trade-offs in other yield-related traits. In addition, the closely linked kompetitive allele-specific PCR (KASP) markers of this locus were developed for marker-assisted selection (MAS) breeding. Four genes within the physical interval were considered as potential candidates based on expression patterns as well as orthologous gene functions. These results laid the foundation for map-based cloning of the gene(s) underlying QSl/Sc.cib-2D.1 and its potential application in wheat ideotype breeding.
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Affiliation(s)
- Mingxiu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- Department of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Yunfang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Donghui Ao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lei Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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16
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Melash AA, Bytyqi B, Nyandi MS, Vad AM, Ábrahám ÉB. Chlorophyll Meter: A Precision Agricultural Decision-Making Tool for Nutrient Supply in Durum Wheat (Triticum turgidum L.) Cultivation under Drought Conditions. Life (Basel) 2023; 13:life13030824. [PMID: 36983979 PMCID: PMC10059945 DOI: 10.3390/life13030824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
How crop biodiversity adapts to drought conditions and enhances grain yield became the most important issue facing agronomists and plant breeders at the turn of the century. Variations in genetic response, inadequacy of nutrients in the soil, and insufficient access to nutrients are factors that aggravate drought stressors. The development of screening tools for identifying drought tolerance is important in the deployment of durum wheat varieties suited to drought-prone environments. An experiment was conducted to evaluate durum wheat varieties under a range of nutrient supplies in naturally imposed drought conditions. The treatments consisting of two nitrogen regimes (i.e., control and 60 kg ha−1), four durum wheat varieties, and three types of nutrients (control, sulfur, and zinc) that were arranged in a split-split plot design with three replications. Both foliar-based sulfur and zinc fertilization were employed at the flag leaf stage, at a rate of 4 and 3-L ha−1, respectively. The results showed a significant (p < 0.05) genetic variation in chlorophyll concentration, grain protein content, tillering potential, and leaf area index. Varieties that contained better leaf chlorophyll content had improved grain yield by about 8.33% under 60 kg/ha nitrogen. A combined application of nitrogen and zinc at flag leaf stage significantly improved grain yield of Duragold by about 21.3%. Leaf chlorophyll content was found to be a more important trait than spikes per m2 to discriminate durum wheat varieties. Foliar application of sulfur increased the grain yield of drought-stressed plants by about 12.23%. Grain yield and protein content were strongly correlated with late-season SPAD readings. Significant (p < 0.05) correlation coefficients were obtained between normalized difference vegetation index, leaf area index, grain yield, and protein content with late-season chlorophyll content, revealing the importance of chlorophyll content in studying and identifying drought-tolerant varieties.
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Affiliation(s)
- Anteneh Agezew Melash
- Kálmán Kerpely Doctoral School of Crop Production and Horticultural Science, University of Debrecen, Böszörményi Street 138, H-4032 Debrecen, Hungary
- Department of Horticulture, College of Agriculture and Environmental Science, Debark University, North Gondar, Debark P.O. Box 90, Ethiopia
- Correspondence:
| | - Bekir Bytyqi
- Kálmán Kerpely Doctoral School of Crop Production and Horticultural Science, University of Debrecen, Böszörményi Street 138, H-4032 Debrecen, Hungary
| | - Muhoja Sylivester Nyandi
- Kálmán Kerpely Doctoral School of Crop Production and Horticultural Science, University of Debrecen, Böszörményi Street 138, H-4032 Debrecen, Hungary
| | - Attila Miklós Vad
- Institutes for Agricultural Research and Educational Farm, University of Debrecen, H-4032 Debrecen, Hungary
| | - Éva Babett Ábrahám
- Institute of Crop Sciences, Faculty of Agricultural, Food Sciences and Environmental Management, University of Debrecen, Böszörményi Street 138, H-4032 Debrecen, Hungary
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17
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Wang Z, Dhakal S, Cerit M, Wang S, Rauf Y, Yu S, Maulana F, Huang W, Anderson JD, Ma XF, Rudd JC, Ibrahim AMH, Xue Q, Hays DB, Bernardo A, St. Amand P, Bai G, Baker J, Baker S, Liu S. QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster. FRONTIERS IN PLANT SCIENCE 2022; 13:1057701. [PMID: 36570880 PMCID: PMC9768232 DOI: 10.3389/fpls.2022.1057701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.
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Affiliation(s)
- Zhen Wang
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Smit Dhakal
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Mustafa Cerit
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shichen Wang
- Genomics and Bioinformatics Service Center, Texas A&M AgriLife Research, College Station, TX, United States
| | - Yahya Rauf
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shuhao Yu
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Frank Maulana
- Noble Research Institute, Ardmore, OK, United States
| | - Wangqi Huang
- Noble Research Institute, Ardmore, OK, United States
| | | | - Xue-Feng Ma
- Noble Research Institute, Ardmore, OK, United States
| | - Jackie C. Rudd
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Amir M. H. Ibrahim
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, United States
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Dirk B. Hays
- Department of Soil and Crop Science, Texas A&M University, College Station, TX, United States
| | - Amy Bernardo
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Paul St. Amand
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Guihua Bai
- Central Small Grain Genotyping Lab and Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Manhattan, KS, United States
| | - Jason Baker
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shannon Baker
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
| | - Shuyu Liu
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX, United States
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18
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Grzebisz W, Diatta J, Barłóg P, Biber M, Potarzycki J, Łukowiak R, Przygocka-Cyna K, Szczepaniak W. Soil Fertility Clock-Crop Rotation as a Paradigm in Nitrogen Fertilizer Productivity Control. PLANTS (BASEL, SWITZERLAND) 2022; 11:2841. [PMID: 36365294 PMCID: PMC9656335 DOI: 10.3390/plants11212841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
The Soil Fertility Clock (SFC) concept is based on the assumption that the critical content (range) of essential nutrients in the soil is adapted to the requirements of the most sensitive plant in the cropping sequence (CS). This provides a key way to effectively control the productivity of fertilizer nitrogen (Nf). The production goals of a farm are set for the maximum crop yield, which is defined by the environmental conditions of the production process. This target can be achieved, provided that the efficiency of Nf approaches 1.0. Nitrogen (in fact, nitrate) is the determining yield-forming factor, but only when it is balanced with the supply of other nutrients (nitrogen-supporting nutrients; N-SNs). The condition for achieving this level of Nf efficiency is the effectiveness of other production factors, including N-SNs, which should be set at ≤1.0. A key source of N-SNs for a plant is the soil zone occupied by the roots. N-SNs should be applied in order to restore their content in the topsoil to the level required by the most sensitive crop in a given CS. Other plants in the CS provide the timeframe for active controlling the distance of the N-SNs from their critical range.
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19
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Peters Haugrud AR, Zhang Q, Green AJ, Xu SS, Faris JD. Identification of stable QTL controlling multiple yield components in a durum × cultivated emmer wheat population under field and greenhouse conditions. G3 (BETHESDA, MD.) 2022; 13:6762085. [PMID: 36250796 PMCID: PMC9911061 DOI: 10.1093/g3journal/jkac281] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Crop yield gains are needed to keep pace with a growing global population and decreasing resources to produce food. Cultivated emmer wheat is a progenitor of durum wheat and a useful source of genetic variation for trait improvement in durum. Here, we evaluated a recombinant inbred line population derived from a cross between the North Dakota durum wheat variety Divide and the cultivated emmer wheat accession PI 272527 consisting of 219 lines. The population was evaluated in 3 field environments and 2 greenhouse experiments to identify quantitative trait locus associated with 11 yield-related traits that were expressed in a consistent manner over multiple environments. We identified 27 quantitative trait locus expressed in at least 2 field environments, 17 of which were also expressed under greenhouse conditions. Seven quantitative trait locus regions on chromosomes 1B, 2A, 2B, 3A, 3B, 6A, and 7B had pleiotropic effects on multiple yield-related traits. The previously cloned genes Q and FT-B1, which are known to be associated with development and morphology, were found to consistently be associated with multiple traits across environments. PI 272527 contributed beneficial alleles for quantitative trait locus associated with multiple traits, especially for seed morphology quantitative trait locus on chromosomes 1B, 2B, and 6A. Three recombinant inbred lines with increased grain size and weight compared to Divide were identified and demonstrated the potential for improvement of durum wheat through deployment of beneficial alleles from the cultivated emmer parent. The findings from this study provide knowledge regarding stable and robust quantitative trait locus that breeders can use for improving yield in durum wheat.
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Affiliation(s)
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Andrew J Green
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Steven S Xu
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Justin D Faris
- Corresponding author: Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND 58102, USA.
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20
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Transcriptional signatures of wheat inflorescence development. Sci Rep 2022; 12:17224. [PMID: 36241895 PMCID: PMC9568521 DOI: 10.1038/s41598-022-21571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
In order to maintain global food security, it will be necessary to increase yields of the cereal crops that provide most of the calories and protein for the world's population, which includes common wheat (Triticum aestivum L.). An important wheat yield component is the number of grain-holding spikelets which form on the spike during inflorescence development. Characterizing the gene regulatory networks controlling the timing and rate of inflorescence development will facilitate the selection of natural and induced gene variants that contribute to increased spikelet number and yield. In the current study, co-expression and gene regulatory networks were assembled from a temporal wheat spike transcriptome dataset, revealing the dynamic expression profiles associated with the progression from vegetative meristem to terminal spikelet formation. Consensus co-expression networks revealed enrichment of several transcription factor families at specific developmental stages including the sequential activation of different classes of MIKC-MADS box genes. This gene regulatory network highlighted interactions among a small number of regulatory hub genes active during terminal spikelet formation. Finally, the CLAVATA and WUSCHEL gene families were investigated, revealing potential roles for TtCLE13, TtWOX2, and TtWOX7 in wheat meristem development. The hypotheses generated from these datasets and networks further our understanding of wheat inflorescence development.
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21
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Gill HS, Halder J, Zhang J, Rana A, Kleinjan J, Amand PS, Bernardo A, Bai G, Sehgal SK. Whole-genome analysis of hard winter wheat germplasm identifies genomic regions associated with spike and kernel traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2953-2967. [PMID: 35939073 DOI: 10.1007/s00122-022-04160-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Genetic dissection of yield component traits including spike and kernel characteristics is essential for the continuous improvement in wheat yield. Genome-wide association studies (GWAS) have been frequently used to identify genetic determinants for spike and kernel-related traits in wheat, though none have been employed in hard winter wheat (HWW) which represents a major class in US wheat acreage. Further, most of these studies relied on assembled diversity panels instead of adapted breeding lines, limiting the transferability of results to practical wheat breeding. Here we assembled a population of advanced/elite breeding lines and well-adapted cultivars and evaluated over four environments for phenotypic analysis of spike and kernel traits. GWAS identified 17 significant multi-environment marker-trait associations (MTAs) for various traits, representing 12 putative quantitative trait loci (QTLs), with five QTLs affecting multiple traits. Four of these QTLs mapped on three chromosomes 1A, 5B, and 7A for spike length, number of spikelets per spike (NSPS), and kernel length are likely novel. Further, a highly significant QTL was detected on chromosome 7AS that has not been previously associated with NSPS and putative candidate genes were identified in this region. The allelic frequencies of important quantitative trait nucleotides (QTNs) were deduced in a larger set of 1,124 accessions which revealed the importance of identified MTAs in the US HWW breeding programs. The results from this study could be directly used by the breeders to select the lines with favorable alleles for making crosses, and reported markers will facilitate marker-assisted selection of stable QTLs for yield components in wheat breeding.
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Affiliation(s)
- Harsimardeep S Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jinfeng Zhang
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Anshul Rana
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Jonathan Kleinjan
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Paul St Amand
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Amy Bernardo
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
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22
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Liu X, Xu Z, Feng B, Zhou Q, Ji G, Guo S, Liao S, Lin D, Fan X, Wang T. Quantitative trait loci identification and breeding value estimation of grain weight-related traits based on a new wheat 50K single nucleotide polymorphism array-derived genetic map. FRONTIERS IN PLANT SCIENCE 2022; 13:967432. [PMID: 36110352 PMCID: PMC9468616 DOI: 10.3389/fpls.2022.967432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
Mining novel and less utilized thousand grain weight (TGW) related genes are useful for improving wheat yield. In this study, a recombinant inbred line population from a cross between Zhongkemai 138 (ZKM138, high TGW) and Chuanmai 44 (CM44, low TGW) was used to construct a new Wheat 50K SNP array-derived genetic map that spanned 1,936.59 cM and contained 4, 139 markers. Based on this map, ninety-one quantitative trait loci (QTL) were detected for eight grain-related traits in six environments. Among 58 QTLs, whose superior alleles were contributed by ZKM138, QTgw.cib-6A was a noticeable major stable QTL and was also highlighted by bulked segregant analysis with RNA sequencing (BSR-Seq). It had a pyramiding effect on TGW enhancement but no significant trade-off effect on grain number per spike or tiller number, with two other QTLs (QTgw.cib-2A.2 and QTgw.cib-6D), possibly explaining the excellent grain performance of ZKM138. After comparison with known loci, QTgw.cib-6A was deduced to be a novel locus that differed from nearby TaGW2 and TaBT1. Seven simple sequence repeat (SSR) and thirty-nine kompetitive allele-specific PCR (KASP) markers were finally developed to narrow the candidate interval of QTgw.cib-6A to 4.1 Mb. Only six genes in this interval were regarded as the most likely candidate genes. QTgw.cib-6A was further validated in different genetic backgrounds and presented 88.6% transmissibility of the ZKM138-genotype and a 16.4% increase of TGW in ZKM138 derivatives. And the geographic pattern of this locus revealed that its superior allele is present in only 6.47% of 433 Chinese modern wheat varieties, indicating its potential contribution to further high-yield breeding.
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Affiliation(s)
- Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaodan Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dian Lin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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23
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Wittern LM, Barrero JM, Bovill WD, Verbyla KL, Hughes T, Swain SM, Steed G, Webb AAR, Gardner K, Greenland A, Jacobs J, Frohberg C, Schmidt RC, Cavanagh C, Rohde A, Davey MW, Hannah MA. Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat. Sci Rep 2022; 12:14229. [PMID: 35987959 PMCID: PMC9392761 DOI: 10.1038/s41598-022-18614-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractTwo homoeologous QTLs for number of spikelets per spike (SPS) were mapped on chromosomes 7AL and 7BL using two wheat MAGIC populations. Sets of lines contrasting for the QTL on 7AL were developed which allowed for the validation and fine mapping of the 7AL QTL and for the identification of a previously described candidate gene, WHEAT ORTHOLOG OF APO1 (WAPO1). Using transgenic overexpression in both a low and a high SPS line, we provide a functional validation for the role of this gene in determining SPS also in hexaploid wheat. We show that the expression levels of this gene positively correlate with SPS in multiple MAGIC founder lines under field conditions as well as in transgenic lines grown in the greenhouse. This work highlights the potential use of WAPO1 in hexaploid wheat for further yield increases. The impact of WAPO1 and SPS on yield depends on other genetic and environmental factors, hence, will require a finely balanced expression level to avoid the development of detrimental pleiotropic phenotypes.
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24
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Liu W, Li Y, Sun Y, Tang J, Che J, Yang S, Wang X, Zhang R, Zhang H. Genetic analysis of morphological traits in spring wheat from the Northeast of China by a genome-wide association study. Front Genet 2022; 13:934757. [PMID: 36061191 PMCID: PMC9434797 DOI: 10.3389/fgene.2022.934757] [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: 05/03/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Identification of the gene for agronomic traits is important for the wheat marker-assisted selection (MAS) breeding. To identify the new and stable loci for agronomic traits, including flag leaf length (FLL), flag leaf width (FLW), uppermost internode length (UIL), and plant morphology (PM, including prostrate, semi-prostrate, and erect). A total of 251 spring wheat accessions collected from the Northeast of China were used to conduct genome-wide association study (GWAS) by 55K SNP arrays. A total of 30 loci for morphological traits were detected, and each explained 4.8–17.9% of the phenotypic variations. Of these, 13 loci have been reported by previous studies, and the other 17 are novel. We have identified seven genes involved in the signal transduction, cell-cycle progression, and plant development pathway as candidate genes. This study provides new insights into the genetic basis of morphological traits. The associated SNPs and accessions with more of favorable alleles identified in this study could be used to promote the wheat breeding progresses.
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Affiliation(s)
- Wenlin Liu
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yuyao Li
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yan Sun
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jingquan Tang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jingyu Che
- KeShan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihaer, China
| | - Shuping Yang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiangyu Wang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Rui Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hongji Zhang
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- *Correspondence: Hongji Zhang,
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25
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Crain J, Larson S, Dorn K, DeHaan L, Poland J. Genetic architecture and QTL selection response for Kernza perennial grain domestication traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2769-2784. [PMID: 35763029 PMCID: PMC9243872 DOI: 10.1007/s00122-022-04148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Analysis of multi-year breeding program data revealed that the genetic architecture of an intermediate wheatgrass population was highly polygenic for both domestication and agronomic traits, supporting the use of genomic selection for new crop domestication. Perennial grains have the potential to provide food for humans and decrease the negative impacts of annual agriculture. Intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®) is a promising perennial grain candidate that The Land Institute has been breeding since 2003. We evaluated four consecutive breeding cycles of IWG from 2016 to 2020 with each cycle containing approximately 1100 unique genets. Using genotyping-by-sequencing markers, quantitative trait loci (QTL) were mapped for 34 different traits using genome-wide association analysis. Combining data across cycles and years, we found 93 marker-trait associations for 16 different traits, with each association explaining 0.8-5.2% of the observed phenotypic variance. Across the four cycles, only three QTL showed an FST differentiation > 0.15 with two corresponding to a decrease in floret shattering. Additionally, one marker associated with brittle rachis was 216 bp from an ortholog of the btr2 gene. Power analysis and quantitative genetic theory were used to estimate the effective number of QTL, which ranged from a minimum of 33 up to 558 QTL for individual traits. This study suggests that key agronomic and domestication traits are under polygenic control and that molecular methods like genomic selection are needed to accelerate domestication and improvement of this new crop.
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Affiliation(s)
- Jared Crain
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA
| | - Steve Larson
- USDA-ARS, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Dorn
- USDA-ARS, Soil Management and Sugarbeet Research, Fort Collins, CO, 80526, USA
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA.
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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26
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Zhang X, Qiao L, Li X, Yang Z, Liu C, Guo H, Zheng J, Zhang S, Chang L, Chen F, Jia J, Yan L, Chang Z. Genetic Incorporation of the Favorable Alleles for Three Genes Associated With Spikelet Development in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:892642. [PMID: 35592560 PMCID: PMC9111956 DOI: 10.3389/fpls.2022.892642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
The number of spikelets per spike is an important trait that directly affects grain yield in wheat. Three quantitative trait loci (QTLs) associated with spikelet nodes per spike (SNS) were mapped in a population of recombinant inbred lines generated from a cross between two advanced breeding lines of winter wheat based on the phenotypic variation evaluated over six locations/years. Two of the three QTLs are QSns.sxau-2A at the WHEATFRIZZY PANICLE (WFZP) loci and QSns.sxau-7A at the WHEAT ORTHOLOG OF APO1 (WAPO1) loci. The WFZP-A1b allele with a 14-bp deletion at QSns.sxau-2A was associated with increased spikelets per spike. WAPO-A1e, as a novel allele at WAPO1, were regulated at the transcript level that was associated with the SNS trait. The third SNS QTL, QSns.sxau-7D on chromosome 7D, was not associated with homoeologous WAPO-D1 or any other genes known to regulate SNS. The favorable alleles for each of WZFP-A1, WAPO-A1, and QSns.sxau-7D are identified and incorporated to increase up to 3.4 spikelets per spike in the RIL lines. Molecular markers for the alleles were developed. This study has advanced our understanding of the genetic basis of natural variation in spikelet development in wheat.
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Affiliation(s)
- Xiaojun Zhang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Linyi Qiao
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Xin Li
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Zujun Yang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Huijuan Guo
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Shuwei Zhang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Lifang Chang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Fang Chen
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Juqing Jia
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Zhijian Chang
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan, China
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Xu X, Li X, Zhang D, Zhao J, Jiang X, Sun H, Ru Z. Identification and validation of QTLs for kernel number per spike and spike length in two founder genotypes of wheat. BMC PLANT BIOLOGY 2022; 22:146. [PMID: 35346053 PMCID: PMC8962171 DOI: 10.1186/s12870-022-03544-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Kernel number per spike (KNS) and spike length (SL) are important spike-related traits in wheat variety improvement. Discovering genetic loci controlling these traits is necessary to elucidate the genetic basis of wheat yield traits and is very important for marker-assisted selection breeding. RESULTS In the present study, we used a recombinant inbred line population with 248 lines derived from the two founder genotypes of wheat, Bima4 and BainongAK58, to construct a high-density genetic map using wheat 55 K genotyping assay. The final genetic linkage map consists of 2356 bin markers (14,812 SNPs) representing all 21 wheat chromosomes, and the entire map spanned 4141.24 cM. A total of 7 and 18 QTLs were identified for KNS and SL, respectively, and they were distributed on 11 chromosomes. The allele effects of the flanking markers for 12 stable QTLs, including four QTLs for KNS and eight QTLs for SL, were estimated based on phenotyping data collected from 15 environments in a diverse wheat panel including 384 elite cultivars and breeding lines. The positive alleles at seven loci, namely, QKns.his-7D2-1, QKns.his-7D2-2, QSl.his-4A-1, QSl.his-5D1, QSl.his-4D2-2, QSl.his-5B and QSl.his-5A-2, significantly increased KNS or SL in the diverse panel, suggesting they are more universal in their effects and are valuable for gene pyramiding in breeding programs. The transmission of Bima4 allele indicated that the favorite alleles at five loci (QKns.his-7D2-1, QSl.his-5A-2, QSl.his-2D1-1, QSl.his-3A-2 and QSl.his-3B) showed a relatively high frequency or an upward trend following the continuity of generations, suggesting that they underwent rigorous selection during breeding. At two loci (QKns.his-7D2-1 and QSl.his-5A-2) that the positive effects of the Bima4 alleles have been validated in the diverse panel, two and one kompetitive allele-specific PCR (KASP) markers were further developed, respectively, and they are valuable for marker-assisted selection breeding. CONCLUSION Important chromosome regions controlling KNS and SL were identified in the founder parents. Our results are useful for knowing the molecular mechanisms of founder parents and future molecular breeding in wheat.
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Affiliation(s)
- Xin Xu
- School of Life Sciences and Basic Medicine, Xinxiang University, Xinxiang, 453003, China
| | - Xiaojun Li
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China.
| | - Dehua Zhang
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Jishun Zhao
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xiaoling Jiang
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Haili Sun
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Zhengang Ru
- School of Life Science and Technology, Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China.
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28
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He F, Wang W, Rutter WB, Jordan KW, Ren J, Taagen E, DeWitt N, Sehgal D, Sukumaran S, Dreisigacker S, Reynolds M, Halder J, Sehgal SK, Liu S, Chen J, Fritz A, Cook J, Brown-Guedira G, Pumphrey M, Carter A, Sorrells M, Dubcovsky J, Hayden MJ, Akhunova A, Morrell PL, Szabo L, Rouse M, Akhunov E. Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat. Nat Commun 2022; 13:826. [PMID: 35149708 PMCID: PMC8837796 DOI: 10.1038/s41467-022-28453-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 01/26/2022] [Indexed: 12/23/2022] Open
Abstract
Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops.
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Affiliation(s)
- Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Wheat Genetic Resources Center, Kansas State University, Manhattan, KS, USA
| | - William B Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, U.S. Vegetable Laboratory, Charleston, SC, USA
| | - Katherine W Jordan
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Ellie Taagen
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA.,USDA-ARS SAA, Plant Science Research, Raleigh, NC, USA
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | | | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Sunish Kumar Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Shuyu Liu
- Texas A&M AgriLife Research, Amarillo, TX, USA
| | - Jianli Chen
- Department of Plant Sciences, University of Idaho, Aberdeen, ID, USA
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Jason Cook
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Gina Brown-Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA.,USDA-ARS SAA, Plant Science Research, Raleigh, NC, USA
| | - Mike Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Arron Carter
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Mark Sorrells
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Matthew J Hayden
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Les Szabo
- USDA-ARS Cereal Disease Lab, St. Paul, MN, USA
| | | | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA. .,Wheat Genetic Resources Center, Kansas State University, Manhattan, KS, USA.
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Bandyopadhyay T, Swarbreck SM, Jaiswal V, Maurya J, Gupta R, Bentley AR, Griffiths H, Prasad M. GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C 4 model Setaria italica (L.). J Adv Res 2022; 42:249-261. [PMID: 36513416 PMCID: PMC9788950 DOI: 10.1016/j.jare.2022.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION N responsiveness is the capacity to perceive and induce morpho-physiological adaptation to external and internal Nitrogen (N). Crop productivity is propelled by N fertilizer and requires the breeding/selection of cultivars with intrinsically high N responsiveness. This trait has many advantages in being more meaningful in commercial/environmental context, facilitating in-season N management and not being inversely correlated with N availability over processes regulating NUE. Current lack of its understanding at the physio-genetic basis is an impediment to select for cultivars with a predictably high N response. OBJECTIVES To dissect physio-genetic basis of N responsiveness in 142 diverse population of foxtail millet, Setaria italica (L.) by employing contrasting N fertilizer nutrition regimes. METHODS We phenotyped S. italica accessions for major yield related traits under low (N10, N25) and optimal (N100) growth conditions and genotyped them to subsequently perform a genome-wide association study to identify genetic loci associated with nitrogen responsiveness trait. Groups of accessions showing contrasting trait performance and allelic forms of specific linked genetic loci (showing haplotypes) were further accessed for N dependent transcript abundances of their proximal genes. RESULTS Our study show that N dependent yield rise in S. italica is driven by grain number whose responsiveness to N availability is genetically underlined. We identify 22 unique SNP loci strongly associated with this trait out of which six exhibit haplotypes and consistent allelic variation between lines with contrasting N dependent grain number response and panicle architectures. Furthermore, differential transcript abundances of specific genes proximally linked to these SNPs in same lines is indicative of their N dependence in a genotype specific manner. CONCLUSION The study demonstrates the value/ potential of N responsiveness as a selection trait and identifies key genetic components underlying the trait in S. italica. This has major implications for improving crop N sustainability and food security.
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Affiliation(s)
| | - Stéphanie M Swarbreck
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Rd, Cambridge CB3 0LE, United Kingdom,Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Vandana Jaiswal
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Rajeev Gupta
- Cereal Crops Research Unit, US Department of Agriculture (USDA) Agricultural Research Service (ARS), Fargo, ND, United States,International Crop Research Institute for the Semi -arid Tropics, Patancheru, Hyderabad, Telangana 502324, India
| | - Alison R. Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Rd, Cambridge CB3 0LE, United Kingdom,International Maize and Wheat Improvement Center, Texcoco, México
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India,Corresponding author at: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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30
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Kuzay S, Lin H, Li C, Chen S, Woods DP, Zhang J, Lan T, von Korff M, Dubcovsky J. WAPO-A1 is the causal gene of the 7AL QTL for spikelet number per spike in wheat. PLoS Genet 2022; 18:e1009747. [PMID: 35025863 PMCID: PMC8791482 DOI: 10.1371/journal.pgen.1009747] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/26/2022] [Accepted: 12/18/2021] [Indexed: 01/08/2023] Open
Abstract
Improving our understanding of the genes regulating grain yield can contribute to the development of more productive wheat varieties. Previously, a highly significant QTL affecting spikelet number per spike (SNS), grain number per spike (GNS) and grain yield was detected on chromosome arm 7AL in multiple genome-wide association studies. Using a high-resolution genetic map, we established that the A-genome homeolog of WHEAT ORTHOLOG OF APO1 (WAPO-A1) was a leading candidate gene for this QTL. Using mutants and transgenic plants, we demonstrate in this study that WAPO-A1 is the causal gene underpinning this QTL. Loss-of-function mutants wapo-A1 and wapo-B1 showed reduced SNS in tetraploid wheat, and the effect was exacerbated in wapo1 combining both mutations. By contrast, spikes of transgenic wheat plants carrying extra copies of WAPO-A1 driven by its native promoter had higher SNS, a more compact spike apical region and a smaller terminal spikelet than the wild type. Taken together, these results indicate that WAPO1 affects SNS by regulating the timing of terminal spikelet formation. Both transgenic and wapo1 mutant plants showed a wide range of floral abnormalities, indicating additional roles of WAPO1 on wheat floral development. Previously, we found three widespread haplotypes in the QTL region (H1, H2 and H3), each associated with particular WAPO-A1 alleles. Results from this and our previous study show that the WAPO-A1 allele in the H1 haplotype (115-bp deletion in the promoter) is expressed at significantly lower levels in the developing spikes than the alleles in the H2 and H3 haplotypes, resulting in reduced SNS. Field experiments also showed that the H2 haplotype is associated with the strongest effects in increasing SNS and GNS (H2>H3>H1). The H2 haplotype is already present in most modern common wheat varieties but is rare in durum wheat, where it might be particularly useful to improve grain yield.
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Affiliation(s)
- Saarah Kuzay
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Chengxia Li
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Shisheng Chen
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Daniel P. Woods
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Tianyu Lan
- Institute for Plant Genetics, Heinrich Heine University, Duesseldorf, Germany
| | - Maria von Korff
- Institute for Plant Genetics, Heinrich Heine University, Duesseldorf, Germany
- Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow’s Needs”, Heinrich Heine University, Duesseldorf, Germany
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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31
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Arriagada O, Gadaleta A, Marcotuli I, Maccaferri M, Campana M, Reveco S, Alfaro C, Matus I, Schwember AR. A comprehensive meta-QTL analysis for yield-related traits of durum wheat ( Triticum turgidum L. var. durum) grown under different water regimes. FRONTIERS IN PLANT SCIENCE 2022; 13:984269. [PMID: 36147234 PMCID: PMC9486101 DOI: 10.3389/fpls.2022.984269] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 05/13/2023]
Abstract
Abiotic stress strongly affects yield-related traits in durum wheat, in particular drought is one of the main environmental factors that have effect on grain yield and plant architecture. In order to obtain new genotypes well adapted to stress conditions, the highest number of desirable traits needs to be combined in the same genotype. In this context, hundreds of quantitative trait loci (QTL) have been identified for yield-related traits in different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies for the reliability of their location and effects. MQTL analysis is a useful method to dissect the genetic architecture of complex traits, which provide an extensive allelic coverage, a higher mapping resolution and allow the identification of putative molecular markers useful for marker-assisted selection (MAS). In the present study, a complete and comprehensive MQTL analysis was carried out to identify genomic regions associated with grain-yield related traits in durum wheat under different water regimes. A total of 724 QTL on all 14 chromosomes (genomes A and B) were collected for the 19 yield-related traits selected, of which 468 were reported under rainfed conditions, and 256 under irrigated conditions. Out of the 590 QTL projected on the consensus map, 421 were grouped into 76 MQTL associated with yield components under both irrigated and rainfed conditions, 12 genomic regions containing stable MQTL on all chromosomes except 1A, 4A, 5A, and 6B. Candidate genes associated to MQTL were identified and an in-silico expression analysis was carried out for 15 genes selected among those that were differentially expressed under drought. These results can be used to increase durum wheat grain yields under different water regimes and to obtain new genotypes adapted to climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari Aldo Moro, Bari, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Matteo Campana
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samantha Reveco
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian Alfaro
- Centro Regional Rayentue, Instituto de Investigaciones Agropecuarias (INIA), Rengo, Chile
| | - Iván Matus
- Centro Regional Quilamapu, Instituto de Investigaciones Agropecuarias (INIA), Chillán, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Andrés R. Schwember,
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Kumar M, Yadav R, Gaikwad KB, Babu P, Kumar Bainsla N, Dharmateja P, Ahmad Chaudhary A, Ansari R. Deciphering the environmental impact on spike architectural traits for grain yield consolidation in bread wheat (T. aestivum L.). Saudi J Biol Sci 2022; 29:2800-2810. [PMID: 35531211 PMCID: PMC9073038 DOI: 10.1016/j.sjbs.2022.01.007] [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: 06/19/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 11/22/2022] Open
Abstract
The realization of grain yield in wheat is decided by source-sink balance under prevailing environmental conditions. Management conditions like changing the sowing time influence the source-sink capacity through modification in agronomic traits. Therefore, this experiment was conducted to decipher the influence of spike architectural traits (SATs) on grain yield and to open avenues for further grain yield enhancement. Comparatively early sowing over timely sowing gives the advantage of realizing higher grain yield with a positive relationship with SATs namely spike length, spikelets per spike, individual spike weight, individual grain weight, number of grains per spikelet, grain length, and grain width of upper and lower spike portion. Confirmatory factorial analysis revealed that spike length, spikelets per spike, individual spike weight, grains per spikelet were having a significant effect in deciding grain yield in early sown. The presence of a significant effect of genotype by environment interaction over grain yield and SATs allows the exploitation of available genotypic and environmental variability for further yield enhancement. GGE analysis on transformed and standardized grain yield-trait (GY-trait) combinations was used in the selection of genotypes having high GY-trait combinations for both sowing times. In early sowing, WG 11 was the best for high GY with high individual spike weight; grain length and grain width at lower and upper parts of the spike; and shorter days to 50% flowering. Genotypes exclusively having the high GY-trait combination along with low values of remaining GY-trait combinations were also selected with genotype focused GGE approach.
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Milner MJ, Bowden S, Craze M, Wallington EJ. Ectopic expression of TaBG1 increases seed size and alters nutritional characteristics of the grain in wheat but does not lead to increased yields. BMC PLANT BIOLOGY 2021; 21:524. [PMID: 34758742 PMCID: PMC8579524 DOI: 10.1186/s12870-021-03294-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Grain size is thought to be a major component of yield in many plant species. Here we set out to understand if knowledge from other cereals such as rice could translate to increased yield gains in wheat and lead to increased nitrogen use efficiency. Previous findings that the overexpression of OsBG1 in rice increased yields while increasing seed size suggest translating gains from rice to other cereals may help to increase yields. RESULTS The orthologous genes of OsBG1 were identified in wheat. One homoeologous wheat gene was cloned and overexpressed in wheat to understand its role in controlling seed size. Potential alteration in the nutritional profile of the grains were also analyzed in wheat overexpressing TaBG1. It was found that increased TaBG1-A expression could indeed lead to larger seed size but was linked to a reduction in seed number per plant leading to no significant overall increase in yield. Other important components of yield such as biomass or tillering did not change significantly with increased TaBG1-A expression. The nutritional profile of the grain was altered, with a significant decrease in the Zn levels in the grain associated with increased seed size, but Fe and Mn concentrations were unchanged. Protein content of the wheat grain also fell under moderate N fertilization levels but not under deficient or adequate levels of N. CONCLUSIONS TaBG1 does control seed size in wheat but increasing the seed size per se does not increase yield and may come at the cost of lower concentrations of essential elements as well as potentially lower protein content. Nevertheless, TaBG1 could be a useful target for further breeding efforts in combination with other genes for increased biomass.
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Affiliation(s)
| | - Sarah Bowden
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
| | - Melanie Craze
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE UK
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Michel S, Löschenberger F, Ametz C, Bürstmayr H. Genomic selection of parents and crosses beyond the native gene pool of a breeding program. THE PLANT GENOME 2021; 14:e20153. [PMID: 34651462 DOI: 10.1002/tpg2.20153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Genomic selection has become a valuable tool for selecting cultivar candidates in many plant breeding programs. Genomic selection of elite parents and crossing combinations with germplasm developed outside a breeding program has, however, hardly been explored until now. The aim of this study was to assess the potential of this method for commonly ranking and selecting elite germplasm developed within and beyond a given breeding program. A winter wheat (Triticum aestivum L.) population consisting of 611 in-house and 87 externally developed lines was used to compare training population compositions and statistical models for genomically predicting baking quality in this framework. Augmenting training populations with lines from other breeding programs had a larger influence on the prediction ability than adding in-house generated lines when aiming to commonly rank both germplasm sets. Exploiting preexisting information of secondary correlated traits resulted likewise in more accurate predictions both in empirical analyses and simulations. Genotyping germplasm developed beyond a given breeding program is moreover a convenient way to clarify its relationships with a breeder's own germplasm because pedigree information is oftentimes not available for this purpose. Genomic predictions can thus support a more informed diversity management, especially when integrating simply to phenotype correlated traits to partly circumvent resource reallocations for a costly phenotyping of germplasm from other programs.
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Affiliation(s)
- Sebastian Michel
- Dep. of Agrobiotechnology, IFA-Tulln, Univ. of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
| | | | - Christian Ametz
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301 Probstdorf, Austria
| | - Hermann Bürstmayr
- Dep. of Agrobiotechnology, IFA-Tulln, Univ. of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430 Tulln, Austria
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Zhu X, Leiser WL, Hahn V, Würschum T. Training set design in genomic prediction with multiple biparental families. THE PLANT GENOME 2021; 14:e20124. [PMID: 34302722 DOI: 10.1002/tpg2.20124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Genomic selection is a powerful tool to reduce the cycle length and enhance the genetic gain of complex traits in plant breeding. However, questions remain about the optimum design and composition of the training set. In this study, we used 944 soybean [Glycine max (L.) Merr.] recombinant inbred lines from eight families derived through a partial-diallel mating design among five parental lines. The cross-validated prediction accuracies for the six traits seed yield, 1,000-seed weight, protein yield, plant height, protein content, and oil content were high, ranging from 0.79 to 0.87. We investigated among-family predictions, making use of the special mating design with different degrees of relatedness among families. Generally, the prediction accuracy decreased from full-sibs to half-sib families to unrelated families. However, half-sib and unrelated families also showed substantial variation in their prediction accuracy for a given family, which appeared to be caused at least in part by the shared segregation of quantitative trait loci in both the training and prediction sets. Combining several half-sib families in composite training sets generally led to an increase in the prediction accuracy compared with the best family alone. The prediction accuracy increased with the size of the training set, but for comparable prediction accuracy, substantially more half-sibs were required than full-sibs. Collectively, our results highlight the potential of genomic selection for soybean breeding and, in a broader context, illustrate the importance of the targeted design of the training set.
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Affiliation(s)
- Xintian Zhu
- State Plant Breeding Institute, Univ. of Hohenheim, Stuttgart, 70593, Germany
| | - Willmar L Leiser
- State Plant Breeding Institute, Univ. of Hohenheim, Stuttgart, 70593, Germany
| | - Volker Hahn
- State Plant Breeding Institute, Univ. of Hohenheim, Stuttgart, 70593, Germany
| | - Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, Univ. of Hohenheim, Stuttgart, 70593, Germany
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Tomar V, Singh D, Dhillon GS, Chung YS, Poland J, Singh RP, Joshi AK, Gautam Y, Tiwari BS, Kumar U. Increased Predictive Accuracy of Multi-Environment Genomic Prediction Model for Yield and Related Traits in Spring Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:720123. [PMID: 34691100 PMCID: PMC8531512 DOI: 10.3389/fpls.2021.720123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Genomic selection (GS) has the potential to improve the selection gain for complex traits in crop breeding programs from resource-poor countries. The GS model performance in multi-environment (ME) trials was assessed for 141 advanced breeding lines under four field environments via cross-predictions. We compared prediction accuracy (PA) of two GS models with or without accounting for the environmental variation on four quantitative traits of significant importance, i.e., grain yield (GRYLD), thousand-grain weight, days to heading, and days to maturity, under North and Central Indian conditions. For each trait, we generated PA using the following two different ME cross-validation (CV) schemes representing actual breeding scenarios: (1) predicting untested lines in tested environments through the ME model (ME_CV1) and (2) predicting tested lines in untested environments through the ME model (ME_CV2). The ME predictions were compared with the baseline single-environment (SE) GS model (SE_CV1) representing a breeding scenario, where relationships and interactions are not leveraged across environments. Our results suggested that the ME models provide a clear advantage over SE models in terms of robust trait predictions. Both ME models provided 2-3 times higher prediction accuracies for all four traits across the four tested environments, highlighting the importance of accounting environmental variance in GS models. While the improvement in PA from SE to ME models was significant, the CV1 and CV2 schemes did not show any clear differences within ME, indicating the ME model was able to predict the untested environments and lines equally well. Overall, our results provide an important insight into the impact of environmental variation on GS in smaller breeding programs where these programs can potentially increase the rate of genetic gain by leveraging the ME wheat breeding trials.
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Affiliation(s)
- Vipin Tomar
- Borlaug Institute for South Asia, Ludhiana, India
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
- International Maize and Wheat Improvement Center, New Delhi, India
| | - Daljit Singh
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Guriqbal Singh Dhillon
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju-si, South Korea
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Ravi Prakash Singh
- Global Wheat Program, International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia, Ludhiana, India
- International Maize and Wheat Improvement Center, New Delhi, India
- Global Wheat Program, International Maize and Wheat Improvement Center, Texcoco, Mexico
| | | | - Budhi Sagar Tiwari
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, India
| | - Uttam Kumar
- Borlaug Institute for South Asia, Ludhiana, India
- International Maize and Wheat Improvement Center, New Delhi, India
- Global Wheat Program, International Maize and Wheat Improvement Center, Texcoco, Mexico
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Irfan Ullah M, Mahpara S, Bibi R, Ullah Shah R, Ullah R, Abbas S, Ihsan Ullah M, Hassan AM, El-Shehawi AM, Brestic M, Zivcak M, Ifnan Khan M. Grain yield and correlated traits of bread wheat lines: Implications for yield improvement. Saudi J Biol Sci 2021; 28:5714-5719. [PMID: 34588882 PMCID: PMC8459068 DOI: 10.1016/j.sjbs.2021.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 04/29/2021] [Accepted: 06/02/2021] [Indexed: 01/10/2023] Open
Abstract
Global wheat yields are suffering due to differences in regional climatic conditions and soil fertility. Plant breeders are continuously working to improve the yield per unit area of wheat crop through selecting superior lines as parents. The screening and field evaluation of available lines allow the selection of superior ones and subsequently improved varieties. Therefore, heritable distinctions among 33 bread wheat lines for yield and related attributes were assessed under field conditions. The experiment included thirty lines and three check varieties. Data relating to different plant characteristics was collected at maturity. Significant differences were recorded for yield and related traits of tested wheat lines and check varieties. Wheat lines V6, V12 and V20 proved better with reduced number of days to reach anthesis and other desirable traits compared to check varieties. Days to start heading had strong correlation with spike length and number of spikelets spike-1. Flag leaf area had positive relationship with peduncle length and yield related traits. The 1000-garin weight and grain yield were also correlated with each other. It is concluded that V6, V10 and V20 proved better for all studied traits than the rest of the lines. Therefore, these lines could be used in wheat breeding program as parents to improve yield.
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Affiliation(s)
- Muhammad Irfan Ullah
- Department of Plant Breeding & Genetics, Ghazi University, Dera Ghazi Khan 32200, Pakistan
| | - Shahzadi Mahpara
- Department of Plant Breeding & Genetics, Ghazi University, Dera Ghazi Khan 32200, Pakistan
| | - Rehana Bibi
- Department of Plant Protection, Ghazi University, Dera Ghazi Khan 32200, Pakistan
| | - Rahmat Ullah Shah
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Rehmat Ullah
- Soil and Water Testing Laboratory for Research, Dera Ghazi Khan 32200, Pakistan
| | - Sibtain Abbas
- Department of Plant Breeding & Genetics, Ghazi University, Dera Ghazi Khan 32200, Pakistan
| | - Muhammad Ihsan Ullah
- Sorghum Research Substation, Department of Agriculture, Dera Ghazi Khan, Pakistan
| | - Aziza M. Hassan
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed M. El-Shehawi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Marian Brestic
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovakia
| | - Marek Zivcak
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovakia
| | - Muhamad Ifnan Khan
- Department of Plant Breeding & Genetics, Ghazi University, Dera Ghazi Khan 32200, Pakistan
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Schierenbeck M, Alqudah AM, Lohwasser U, Tarawneh RA, Simón MR, Börner A. Genetic dissection of grain architecture-related traits in a winter wheat population. BMC PLANT BIOLOGY 2021; 21:417. [PMID: 34507551 PMCID: PMC8431894 DOI: 10.1186/s12870-021-03183-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/20/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND The future productivity of wheat (T. aestivum L.) as the most grown crop worldwide is of utmost importance for global food security. Thousand kernel weight (TKW) in wheat is closely associated with grain architecture-related traits, e.g. kernel length (KL), kernel width (KW), kernel area (KA), kernel diameter ratio (KDR), and factor form density (FFD). Discovering the genetic architecture of natural variation in these traits, identifying QTL and candidate genes are the main aims of this study. Therefore, grain architecture-related traits in 261 worldwide winter accessions over three field-year experiments were evaluated. RESULTS Genome-wide association analysis using 90K SNP array in FarmCPU model revealed several interesting genomic regions including 17 significant SNPs passing false discovery rate threshold and strongly associated with the studied traits. Four of associated SNPs were physically located inside candidate genes within LD interval e.g. BobWhite_c5872_589 (602,710,399 bp) found to be inside TraesCS6A01G383800 (602,699,767-602,711,726 bp). Further analysis reveals the four novel candidate genes potentially involved in more than one grain architecture-related traits with a pleiotropic effects e.g. TraesCS6A01G383800 gene on 6A encoding oxidoreductase activity was associated with TKW and KA. The allelic variation at the associated SNPs showed significant differences betweeen the accessions carying the wild and mutated alleles e.g. accessions carying C allele of BobWhite_c5872_589, TraesCS6A01G383800 had significantly higher TKW than the accessions carying T allele. Interestingly, these genes were highly expressed in the grain-tissues, demonstrating their pivotal role in controlling the grain architecture. CONCLUSIONS These results are valuable for identifying regions associated with kernel weight and dimensions and potentially help breeders in improving kernel weight and architecture-related traits in order to increase wheat yield potential and end-use quality.
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Affiliation(s)
- Matías Schierenbeck
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, D-06466, Seeland, Germany.
- Cereals, Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina.
- CONICET CCT La Plata. La Plata, Buenos Aires, Argentina.
| | - Ahmad M Alqudah
- Department of Agroecology, Aarhus University at Flakkebjerg, Forsøgsvej 1, 4200, Slagelse, Denmark.
| | - Ulrike Lohwasser
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, D-06466, Seeland, Germany
| | - Rasha A Tarawneh
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, D-06466, Seeland, Germany
| | - María Rosa Simón
- Cereals, Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata. La Plata, Buenos Aires, Argentina
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, D-06466, Seeland, Germany
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Snowdon RJ, Wittkop B, Chen TW, Stahl A. Crop adaptation to climate change as a consequence of long-term breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1613-1623. [PMID: 33221941 PMCID: PMC8205907 DOI: 10.1007/s00122-020-03729-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/11/2020] [Indexed: 05/09/2023]
Abstract
Major global crops in high-yielding, temperate cropping regions are facing increasing threats from the impact of climate change, particularly from drought and heat at critical developmental timepoints during the crop lifecycle. Research to address this concern is frequently focused on attempts to identify exotic genetic diversity showing pronounced stress tolerance or avoidance, to elucidate and introgress the responsible genetic factors or to discover underlying genes as a basis for targeted genetic modification. Although such approaches are occasionally successful in imparting a positive effect on performance in specific stress environments, for example through modulation of root depth, major-gene modifications of plant architecture or function tend to be highly context-dependent. In contrast, long-term genetic gain through conventional breeding has incrementally increased yields of modern crops through accumulation of beneficial, small-effect variants which also confer yield stability via stress adaptation. Here we reflect on retrospective breeding progress in major crops and the impact of long-term, conventional breeding on climate adaptation and yield stability under abiotic stress constraints. Looking forward, we outline how new approaches might complement conventional breeding to maintain and accelerate breeding progress, despite the challenges of climate change, as a prerequisite to sustainable future crop productivity.
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Affiliation(s)
- Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany.
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Tsu-Wei Chen
- Albrecht Daniel Thaer Institute of Agricultural and Horticultural Sciences, Humboldt University Berlin, Lentzeallee 75, 14195, Berlin, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
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Corsi B, Obinu L, Zanella CM, Cutrupi S, Day R, Geyer M, Lillemo M, Lin M, Mazza L, Percival-Alwyn L, Stadlmeier M, Mohler V, Hartl L, Cockram J. Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1435-1454. [PMID: 33712876 PMCID: PMC8081691 DOI: 10.1007/s00122-021-03781-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/20/2021] [Indexed: 05/26/2023]
Abstract
KEY MESSAGE Quantitative trait locus (QTL) mapping of 15 yield component traits in a German multi-founder population identified eight QTL each controlling ≥2 phenotypes, including the genetic loci Rht24, WAPO-A1 and WAPO-B1. Grain yield in wheat (Triticum aestivum L.) is a polygenic trait representing the culmination of many developmental processes and their interactions with the environment. Toward maintaining genetic gains in yield potential, 'reductionist approaches' are commonly undertaken by which the genetic control of yield components, that collectively determine yield, are established. Here we use an eight-founder German multi-parental wheat population to investigate the genetic control and phenotypic trade-offs between 15 yield components. Increased grains per ear was significantly positively correlated with the number of fertile spikelets per ear and negatively correlated with the number of infertile spikelets. However, as increased grain number and fertile spikelet number per ear were significantly negatively correlated with thousand grain weight, sink strength limitations were evident. Genetic mapping identified 34 replicated quantitative trait loci (QTL) at two or more test environments, of which 24 resolved into eight loci each controlling two or more traits-termed here 'multi-trait QTL' (MT-QTL). These included MT-QTL associated with previously cloned genes controlling semi-dwarf plant stature, and with the genetic locus Reduced height 24 (Rht24) that further modulates plant height. Additionally, MT-QTL controlling spikelet number traits were located to chromosome 7A encompassing the gene WHEAT ORTHOLOG OF APO1 (WAPO-A1), and to its homoeologous location on chromosome 7B containing WAPO-B1. The genetic loci identified in this study, particularly those that potentially control multiple yield components, provide future opportunities for the targeted investigation of their underlying genes, gene networks and phenotypic trade-offs, in order to underpin further genetic gains in yield.
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Affiliation(s)
| | - Lia Obinu
- Department of Agriculture, University of Sassari, Viale Italia, 07100, Sassari, Italy
| | | | | | - Rob Day
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Morten Lillemo
- Norwegian University of Life Sciences (NMBU), P.O. Box 5003, NO-1432, Ås, Norway
| | - Min Lin
- Norwegian University of Life Sciences (NMBU), P.O. Box 5003, NO-1432, Ås, Norway
| | | | | | - Melanie Stadlmeier
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
- Saatzucht Donau GesmbH and Co KG, Mendelweg 1, 4981, Reichersberg, Austria
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
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Mora‐Ramirez I, Weichert H, von Wirén N, Frohberg C, de Bodt S, Schmidt R, Weber H. The da1 mutation in wheat increases grain size under ambient and elevated CO 2 but not grain yield due to trade-off between grain size and grain number. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2021; 2:61-73. [PMID: 37284283 PMCID: PMC10168082 DOI: 10.1002/pei3.10041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 06/08/2023]
Abstract
Grain size is potentially yield determining in wheat, controlled by the ubiquitin pathway and negatively regulated by ubiquitin receptor DA1. We analyzed whether increased thousand grain weight in wheat da1 mutant is translated into higher grain yield and whether additional carbon provided by elevated (e)CO2 can be better used by the da1, displaying higher grain sink strength and size. Yield-related, biomass, grain quality traits, and grain dimensions were analyzed by two-factorial mixed-model analysis, regarding genotype and eCO2. da1 increased grain size but reduced spikes and grains per plant, grains per spike, and spikelets per spike, independent of eCO2 treatment, leaving total grain yield unchanged. eCO2 increased yield and grain number additively and independently of da1 but did not overcome the trade-off between grain size and number observed for da1. eCO2 but not da1 impaired grain quality, strongly decreasing concentrations of several macroelement and microelement. In conclusion, intrinsic stimulation of grain sink strength and grain size, achieved by da1, is not benefitting total yield unless trade-offs between grain size and numbers can be overcome. The results reveal interactions of yield components in da1-wheat under ambient and eCO2, thereby uncovering limitations enhancing wheat yield potential.
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Affiliation(s)
- Isabel Mora‐Ramirez
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)GaterslebenGermany
| | - Heiko Weichert
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)GaterslebenGermany
| | - Nicolaus von Wirén
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)GaterslebenGermany
| | | | | | | | - Hans Weber
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)GaterslebenGermany
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Wheat Developmental Traits as Affected by the Interaction between Eps-7D and Temperature under Contrasting Photoperiods with Insensitive Ppd-D1 Background. PLANTS 2021; 10:plants10030547. [PMID: 33805828 PMCID: PMC7999118 DOI: 10.3390/plants10030547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 01/14/2023]
Abstract
Earliness per se (Eps) genes are important to fine tune adaptation, and studying their probable pleiotropic effect on wheat yield traits is worthwhile. In addition, it has been shown that some Eps genes interact with temperature and therefore determining the likely Eps × temperature interaction is needed for each newly identified Eps gene. We studied two NILs differing in the newly identified Eps-7D (carrying insensitive Ppd-D1 in the background) under three temperature regimes (9, 15 and 18 °C) and two photoperiods (12 and 24 h). Eps-7D affected time to anthesis as expected and the Eps-7D-late allele extended both the period before and after terminal spikelet. The interaction effect of Eps-7D × temperature was significant but not cross-over: the magnitude and level of significance of the difference between NILs with the late or early allele was affected by the growing temperature (i.e., difference was least at 18 °C and largest at 9 °C), and the differences caused due to temperature sensitivity were influenced by photoperiod. The rate of leaf initiation was faster in NIL with Eps-7D-early than with the late allele which compensated for the shorter duration of leaf initiation resulting in similar final leaf number between two NILs. Eps-7D-late consistently increased spike fertility through improving floret primordia survival as a consequence of extending the late reproductive phase.
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Zhou H, Riche AB, Hawkesford MJ, Whalley WR, Atkinson BS, Sturrock CJ, Mooney SJ. Determination of wheat spike and spikelet architecture and grain traits using X-ray Computed Tomography imaging. PLANT METHODS 2021; 17:26. [PMID: 33750418 PMCID: PMC7945051 DOI: 10.1186/s13007-021-00726-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/26/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Wheat spike architecture is a key determinant of multiple grain yield components and detailed examination of spike morphometric traits is beneficial to explain wheat grain yield and the effects of differing agronomy and genetics. However, quantification of spike morphometric traits has been very limited because it relies on time-consuming manual measurements. RESULTS In this study, using X-ray Computed Tomography imaging, we proposed a method to efficiently detect the 3D architecture of wheat spikes and component spikelets by clustering grains based on their Euclidean distance and relative positions. Morphometric characteristics of wheat spikelets and grains, e.g., number, size and spatial distribution along the spike can be determined. Two commercial wheat cultivars, one old, Maris Widgeon, and one modern, Siskin, were studied as examples. The average grain volume of Maris Widgeon and Siskin did not differ, but Siskin had more grains per spike and therefore greater total grain volume per spike. The spike length and spikelet number were not statistically different between the two cultivars. However, Siskin had a higher spikelet density (number of spikelets per unit spike length), with more grains and greater grain volume per spikelet than Maris Widgeon. Spatial distribution analysis revealed the number of grains, the average grain volume and the total grain volume of individual spikelets varied along the spike. Siskin had more grains and greater grain volumes per spikelet from spikelet 6, but not spikelet 1-5, compared with Maris Widgeon. The distribution of average grain volume along the spike was similar for the two wheat cultivars. CONCLUSION The proposed method can efficiently extract spike, spikelet and grain morphometric traits of different wheat cultivars, which can contribute to a more detailed understanding of the sink of wheat grain yield.
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Affiliation(s)
- Hu Zhou
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | | | | | | | - Brian S. Atkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | - Craig J. Sturrock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | - Sacha J. Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
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Li T, Deng G, Tang Y, Su Y, Wang J, Cheng J, Yang Z, Qiu X, Pu X, Zhang H, Liang J, Yu M, Wei Y, Long H. Identification and Validation of a Novel Locus Controlling Spikelet Number in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:611106. [PMID: 33719283 PMCID: PMC7952655 DOI: 10.3389/fpls.2021.611106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/29/2021] [Indexed: 05/24/2023]
Abstract
Spikelet number is an important target trait for wheat yield improvement. Thus, the identification and verification of novel quantitative trait locus (QTL)/genes controlling spikelet number are essential for dissecting the underlying molecular mechanisms and hence for improving grain yield. In the present study, we constructed a high-density genetic map for the Kechengmai1/Chuanmai42 doubled haploid (DH) population using 13,068 single-nucleotide polymorphism (SNP) markers from the Wheat 55K SNP array. A comparison between the genetic and physical maps indicated high consistence of the marker orders. Based on this genetic map, a total of 27 QTLs associated with total spikelet number per spike (TSN) and fertile spikelet number per spike (FSN) were detected on chromosomes 1B, 1D, 2B, 2D, 3D, 4A, 4D, 5A, 5B, 5D, 6A, 6B, and 7D in five environments. Among them, five QTLs on chromosome 2D, 3D, 5A, and 7D were detected in multiple environments and combined QTL analysis, explaining the phenotypic variance ranging from 3.64% to 23.28%. Particularly, QTsn/Fsn.cib-3D for TSN and FSN [phenotypic variation explained (PVE) = 5.97-23.28%, limit of detection (LOD) = 3.73-18.51] is probably a novel locus and located in a 4.5-cM interval on chromosome arm 3DL flanking by the markers AX-110914105 and AX-109429351. This QTL was further validated in other two populations with different genetic backgrounds using the closely linked Kompetitive Allele-Specific PCR (KASP) marker KASP_AX-110914105. The results indicated that QTsn/Fsn.cib-3D significantly increased the TSN (5.56-7.96%) and FSN (5.13-9.35%), which were significantly correlated with grain number per spike (GNS). We also preliminary analyzed the candidate genes within this locus by sequence similarity, spatial expression patterns, and collinearity analysis. These results provide solid foundation for future fine mapping and cloning of QTsn/Fsn.cib-3D. The developed and validated KASP markers could be utilized in molecular breeding aiming to increase the grain yield in wheat.
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Affiliation(s)
- Tao Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jie Cheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xuebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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45
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Alotaibi F, Alharbi S, Alotaibi M, Al Mosallam M, Motawei M, Alrajhi A. Wheat omics: Classical breeding to new breeding technologies. Saudi J Biol Sci 2021; 28:1433-1444. [PMID: 33613071 PMCID: PMC7878716 DOI: 10.1016/j.sjbs.2020.11.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 12/26/2022] Open
Abstract
Wheat is an important cereal crop, and its significance is more due to compete for dietary products in the world. Many constraints facing by the wheat crop due to environmental hazardous, biotic, abiotic stress and heavy matters factors, as a result, decrease the yield. Understanding the molecular mechanism related to these factors is significant to figure out genes regulate under specific conditions. Classical breeding using hybridization has been used to increase the yield but not prospered at the desired level. With the development of newly emerging technologies in biological sciences i.e., marker assisted breeding (MAB), QTLs mapping, mutation breeding, proteomics, metabolomics, next-generation sequencing (NGS), RNA_sequencing, transcriptomics, differential expression genes (DEGs), computational resources and genome editing techniques i.e. (CRISPR cas9; Cas13) advances in the field of omics. Application of new breeding technologies develops huge data; considerable development is needed in bioinformatics science to interpret the data. However, combined omics application to address physiological questions linked with genetics is still a challenge. Moreover, viroid discovery opens the new direction for research, economics, and target specification. Comparative genomics important to figure gene of interest processes are further discussed about considering the identification of genes, genomic loci, and biochemical pathways linked with stress resilience in wheat. Furthermore, this review extensively discussed the omics approaches and their effective use. Integrated plant omics technologies have been used viroid genomes associated with CRISPR and CRISPR-associated Cas13a proteins system used for engineering of viroid interference along with high-performance multidimensional phenotyping as a significant limiting factor for increasing stress resistance in wheat.
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Affiliation(s)
- Fahad Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Saif Alharbi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Majed Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Mobarak Al Mosallam
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | | | - Abdullah Alrajhi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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Amalova A, Abugalieva S, Chudinov V, Sereda G, Tokhetova L, Abdikhalyk A, Turuspekov Y. QTL mapping of agronomic traits in wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan. PeerJ 2021; 9:e10733. [PMID: 33643705 PMCID: PMC7897413 DOI: 10.7717/peerj.10733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/17/2020] [Indexed: 12/01/2022] Open
Abstract
Background The success of wheat production is largely dependent on local breeding projects that focus on the development of high-yielding cultivars with the use of novel molecular tools. One strategy for improving wheat productivity involves the deployment of diverse germplasms with a high potential yield. An important factor for achieving success involves the dissection of quantitative trait loci (QTLs) for complex agronomic traits, such as grain yield components, in targeted environments for wheat growth. Methods In this study, we tested the United Kingdom (UK) spring set of the doubled haploid (DH) reference population derived from the cross between two British cultivars, Avalon (winter wheat) and Cadenza (spring wheat), in the Northern, Central, and Southern regions (Karabalyk, Karaganda, Kyzylorda) of Kazakhstan over three years (2013–2015). The DH population has previously been genotyped by UK scientists using 3647 polymorphic DNA markers. The list of tested traits includes the heading time, seed maturation time, plant height, spike length, productive tillering, number of kernels per spike, number of kernels per meter, thousand kernel weight, and yield per square meter. Windows QTL Cartographer was applied for QTL mapping using the composite interval mapping method. Results In total, 83 out of 232 QTLs were identified as stable QTLs from at least two environments. A literature survey suggests that 40 QTLs had previously been reported elsewhere, indicating that this study identified 43 QTLs that are presumably novel marker-trait associations (MTA) for these environments. Hence, the phenotyping of the DH population in new environments led to the discovery of novel MTAs. The identified SNP markers associated with agronomic traits in the DH population could be successfully used in local Kazakh breeding projects for the improvement of wheat productivity.
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Affiliation(s)
- Akerke Amalova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Vladimir Chudinov
- Karabalyk Agricultural Experimental Station, Nauchnoe, Kostanai Region, Kazakhstan
| | - Grigoriy Sereda
- Karaganda Research Institute of Agriculture, Karaganda, Kazakhstan
| | | | - Alima Abdikhalyk
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Faculty of Agrobiology, Kazakh National Agrarian University, Almaty, Kazakhstan
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Elhadi GMI, Kamal NM, Gorafi YSA, Yamasaki Y, Takata K, Tahir ISA, Itam MO, Tanaka H, Tsujimoto H. Exploitation of Tolerance of Wheat Kernel Weight and Shape-Related Traits from Aegilops tauschii under Heat and Combined Heat-Drought Stresses. Int J Mol Sci 2021; 22:1830. [PMID: 33673217 PMCID: PMC7917938 DOI: 10.3390/ijms22041830] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 12/25/2022] Open
Abstract
Kernel weight and shape-related traits are inherited stably and increase wheat yield. Narrow genetic diversity limits the progress of wheat breeding. Here, we evaluated kernel weight and shape-related traits and applied genome-wide association analysis to a panel of wheat multiple synthetic derivative (MSD) lines. The MSD lines harbored genomic fragments from Aegilops tauschii. These materials were grown under optimum conditions in Japan, as well as under heat and combined heat-drought conditions in Sudan. We aimed to explore useful QTLs for kernel weight and shape-related traits under stress conditions. These can be useful for enhancing yield under stress conditions. MSD lines possessed remarkable genetic variation for all traits under all conditions, and some lines showed better performance than the background parent Norin 61. We identified 82 marker trait associations (MTAs) under the three conditions; most of them originated from the D genome. All of the favorable alleles originated from Ae. tauschii. For the first time, we identified markers on chromosome 5D associated with a candidate gene encoding a RING-type E3 ubiquitin-protein ligase and expected to have a role in regulating wheat seed size. Our study provides important knowledge for the improvement of wheat yield under optimum and stress conditions. The results emphasize the importance of Ae. tauschii as a gene reservoir for wheat breeding.
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Affiliation(s)
- Gamila Mohamed Idris Elhadi
- United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan; (G.M.I.E.); (M.O.I.)
| | - Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Yuji Yamasaki
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
| | - Kanenori Takata
- National Agriculture and Food Research Organization, Fukuyama 721-8514, Japan;
| | - Izzat S. A. Tahir
- Wheat Research Program, Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan;
| | - Michel O. Itam
- United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan; (G.M.I.E.); (M.O.I.)
| | - Hiroyuki Tanaka
- Faculty of Agriculture, Tottori University, Tottori 680-8550, Japan;
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan; (N.M.K.); (Y.S.A.G.); (Y.Y.)
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48
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Brassac J, Muqaddasi QH, Plieske J, Ganal MW, Röder MS. Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike. Sci Rep 2021; 11:1585. [PMID: 33452357 PMCID: PMC7811022 DOI: 10.1038/s41598-020-80473-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/17/2020] [Indexed: 11/21/2022] Open
Abstract
Total spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.
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Affiliation(s)
- Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany.
| | - Quddoos H Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany.,European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Jörg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany
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49
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Koua AP, Oyiga BC, Baig MM, Léon J, Ballvora A. Breeding Driven Enrichment of Genetic Variation for Key Yield Components and Grain Starch Content Under Drought Stress in Winter Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:684205. [PMID: 34484257 PMCID: PMC8415485 DOI: 10.3389/fpls.2021.684205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/20/2021] [Indexed: 05/12/2023]
Abstract
Drought is one of the major abiotic stress factors limiting wheat production worldwide, thus threatening food security. The dissection of the genetic footprint of drought stress response offers strong opportunities toward understanding and improving drought tolerance (DT) in wheat. In this study, we investigated the genotypic variability for drought response among 200 diverse wheat cultivars (genotypes) using agronomic, developmental, and grain quality traits (GQT), and conducted genome-wide association studies (GWAS) to uncover the genetic architectures of these important traits. Results indicated significant effects of genotype, water regime and their interactions for all agronomic traits. Grain yield (GY) was the most drought-responsive trait and was highly correlated with kernels number per meter square (KN). Genome-wide association studies revealed 17 and 20 QTL regions under rainfed and drought conditions, respectively, and identified one LD block on chromosome 3A and two others on 5D associated with breeding progress (BP). The major haplotypes of these LD blocks have been positively selected through breeding and are associated with higher starch accumulation and GY under drought conditions. Upon validation, the identified QTL regions caring favorable alleles for high starch and yield will shed light on mechanisms of tolerance to drought and can be used to develop drought resistant cultivars.
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Affiliation(s)
- Ahossi Patrice Koua
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Benedict Chijioke Oyiga
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Mirza Majid Baig
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Jens Léon
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
- Field Lab Campus Klein-Altendorf, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Agim Ballvora
- Department of Plant Breeding, Institut für Nutzpflanzenwissenschaften und Ressourcenschutz (INRES), Rheinische Friedrich-Wilhelms-University, Bonn, Germany
- *Correspondence: Agim Ballvora
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50
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Li D, Zhou Z, Lu X, Jiang Y, Li G, Li J, Wang H, Chen S, Li X, Würschum T, Reif JC, Xu S, Li M, Liu W. Genetic Dissection of Hybrid Performance and Heterosis for Yield-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:774478. [PMID: 34917109 PMCID: PMC8670227 DOI: 10.3389/fpls.2021.774478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/01/2021] [Indexed: 05/14/2023]
Abstract
Heterosis contributes a big proportion to hybrid performance in maize, especially for grain yield. It is attractive to explore the underlying genetic architecture of hybrid performance and heterosis. Considering its complexity, different from former mapping method, we developed a series of linear mixed models incorporating multiple polygenic covariance structures to quantify the contribution of each genetic component (additive, dominance, additive-by-additive, additive-by-dominance, and dominance-by-dominance) to hybrid performance and midparent heterosis variation and to identify significant additive and non-additive (dominance and epistatic) quantitative trait loci (QTL). Here, we developed a North Carolina II population by crossing 339 recombinant inbred lines with two elite lines (Chang7-2 and Mo17), resulting in two populations of hybrids signed as Chang7-2 × recombinant inbred lines and Mo17 × recombinant inbred lines, respectively. The results of a path analysis showed that kernel number per row and hundred grain weight contributed the most to the variation of grain yield. The heritability of midparent heterosis for 10 investigated traits ranged from 0.27 to 0.81. For the 10 traits, 21 main (additive and dominance) QTL for hybrid performance and 17 dominance QTL for midparent heterosis were identified in the pooled hybrid populations with two overlapping QTL. Several of the identified QTL showed pleiotropic effects. Significant epistatic QTL were also identified and were shown to play an important role in ear height variation. Genomic selection was used to assess the influence of QTL on prediction accuracy and to explore the strategy of heterosis utilization in maize breeding. Results showed that treating significant single nucleotide polymorphisms as fixed effects in the linear mixed model could improve the prediction accuracy under prediction schemes 2 and 3. In conclusion, the different analyses all substantiated the different genetic architecture of hybrid performance and midparent heterosis in maize. Dominance contributes the highest proportion to heterosis, especially for grain yield, however, epistasis contributes the highest proportion to hybrid performance of grain yield.
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Affiliation(s)
- Dongdong Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohuan Lu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Guoliang Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Junhui Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Haoying Wang
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shaojiang Chen
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Wenxin Liu,
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Mingshun Li,
| | - Wenxin Liu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Shizhong Xu,
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