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Bian Y, Li L, Tian X, Xu D, Sun M, Li F, Xie L, Liu S, Liu B, Xia X, He Z, Cao S. Rht12b, a widely used ancient allele of TaGA2oxA13, reduces plant height and enhances yield potential in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:253. [PMID: 37989964 DOI: 10.1007/s00122-023-04502-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
KEY MESSAGE We identified a new wheat dwarfing allele Rht12b conferring reduced height and higher grain yield, pinpointed its causal variations, developed a breeding-applicable marker, and traced its origin and worldwide distribution. Plant height control is essential to optimize lodging resistance and yield gain in crops. RHT12 is a reduced height (Rht) locus that is identified in a mutationally induced dwarfing mutant and encodes a gibberellin 2-oxidase TaGA2oxA13. However, the artificial dwarfing allele is not used in wheat breeding due to excessive height reduction. Here, we confirmed a stable Rht locus, overlapping with RHT12, in a panel of wheat cultivars and its dwarfing allele reduced plant height by 5.4-8.2 cm, equivalent to Rht12b, a new allele of RHT12. We validated the effect of Rht12b on plant height in a bi-parent mapping population. Importantly, wheat cultivars carrying Rht12b had higher grain yield than those with the contrasting Rht12a allele. Rht12b conferred higher expression level of TaGA2oxA13. Transient activation assays defined SNP-390(C/A) in the promoter of TaGA2oxA13 as the causal variation. An efficient kompetitive allele-specific PCR marker was developed to diagnose Rht12b. Conjoint analysis showed that Rht12b plus the widely used Rht-D1b, Rht8 and Rht24b was the predominant Rht combination and conferred a moderate plant height in tested wheat cultivars. Evolutionary tracking uncovered that RHT12 locus arose from a tandem duplication event with Rht12b firstly appearing in wild emmer. The frequency of Rht12b was approximately 70% (700/1005) in a worldwide wheat panel and comparable to or higher than those of other widely used Rht genes, suggesting it had been subjected to positive selection. These findings not only identify a valuable Rht gene for wheat improvement but also develop a functionally diagnostic tool for marker-assisted breeding.
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Affiliation(s)
- Yingjie Bian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lingli Li
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xiuling Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Mengjing Sun
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Faji Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Lina Xie
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Siyang Liu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Bingyan Liu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center China Office, c/o Chinese Academy Agricultural Sciences, Beijing, 100081, China.
| | - Shuanghe Cao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Manjunatha PB, Aski MS, Mishra GP, Gupta S, Devate NB, Singh A, Bansal R, Kumar S, Nair RM, Dikshit HK. Genome-wide association studies for phenological and agronomic traits in mungbean ( Vigna radiata L. Wilczek). FRONTIERS IN PLANT SCIENCE 2023; 14:1209288. [PMID: 37810385 PMCID: PMC10558178 DOI: 10.3389/fpls.2023.1209288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023]
Abstract
Mungbean (Vigna radiata L. Wilczek) is one of the important warm-season food legumes, contributing substantially to nutritional security and environmental sustainability. The genetic complexity of yield-associated agronomic traits in mungbean is not well understood. To dissect the genetic basis of phenological and agronomic traits, we evaluated 153 diverse mungbean genotypes for two phenological (days to heading and days to maturity) and eight agronomic traits (leaf nitrogen status using SPAD, plant height, number of primary branches, pod length, number of pods per plant, seeds per pod, 100-seed weight, and yield per plant) under two environmental conditions. A wide array of phenotypic variability was apparent among the studied genotypes for all the studied traits. The broad sense of heritability of traits ranged from 0.31 to 0.95 and 0.21 to 0.94 at the Delhi and Ludhiana locations, respectively. A total of 55,634 genome-wide single nucleotide polymorphisms (SNPs) were obtained by the genotyping-by-sequencing method, of which 15,926 SNPs were retained for genome-wide association studies (GWAS). GWAS with Bayesian information and linkage-disequilibrium iteratively nested keyway (BLINK) model identified 50 SNPs significantly associated with phenological and agronomic traits. In total, 12 SNPs were found to be significantly associated with phenological traits across environments, explaining 7%-18.5% of phenotypic variability, and 38 SNPs were significantly associated with agronomic traits, explaining 4.7%-27.6% of the phenotypic variability. The maximum number of SNPs (15) were located on chromosome 1, followed by seven SNPs each on chromosomes 2 and 8. The BLAST search identified 19 putative candidate genes that were involved in light signaling, nitrogen responses, phosphorus (P) transport and remobilization, photosynthesis, respiration, metabolic pathways, and regulating growth and development. Digital expression analysis of 19 genes revealed significantly higher expression of 12 genes, viz. VRADI01G08170, VRADI11G09170, VRADI02G00450, VRADI01G00700, VRADI07G14240, VRADI03G06030, VRADI02G14230, VRADI08G01540, VRADI09G02590, VRADI08G00110, VRADI02G14240, and VRADI02G00430 in the roots, cotyledons, seeds, leaves, shoot apical meristems, and flowers. The identified SNPs and putative candidate genes provide valuable genetic information for fostering genomic studies and marker-assisted breeding programs that improve yield and agronomic traits in mungbean.
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Affiliation(s)
- P. B. Manjunatha
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar S. Aski
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Gyan Prakash Mishra
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Soma Gupta
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Narayana Bhat Devate
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Akanksha Singh
- Amity Institute of Organic Agriculture, Amity University, Noida, India
| | - Ruchi Bansal
- Division of Plant Physiology, ICAR- Indian Agricultural Research Institute, New Delhi, India
| | - Shiv Kumar
- International Centre for Agricultural Research in the Dry Areas (ICARDA), New Delhi, India
| | | | - Harsh Kumar Dikshit
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, India
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Qin R, Ma T, Cai Y, Shi X, Cheng J, Dong J, Wang C, Li S, Pan G, Guan Y, Zhang L, Yang S, Xu H, Zhao C, Sun H, Li X, Wu Y, Li J, Cui F. Characterization and fine mapping analysis of a major stable QTL qKnps-4A for kernel number per spike in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:211. [PMID: 37737910 DOI: 10.1007/s00122-023-04456-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023]
Abstract
KEY MESSAGE A major stable QTL for kernel number per spike was narrowed down to a 2.19-Mb region containing two potential candidate genes, and its effects on yield-related traits were characterized. Kernel number per spike (KNPS) in wheat is a key yield component. Dissection and characterization of major stable quantitative trait loci (QTLs) for KNPS would be of considerable value for the genetic improvement of yield potential using molecular breeding technology. We had previously reported a major stable QTL controlling KNPS, qKnps-4A. In the current study, primary fine-mapping analysis, based on the primary mapping population, located qKnps-4A to an interval of approximately 6.8-Mb from 649.0 to 655.8 Mb on chromosome 4A refering to 'Kenong 9204' genome. Further fine-mapping analysis based on a secondary mapping population narrowed qKnps-4A to an approximately 2.19-Mb interval from 653.72 to 655.91 Mb. Transcriptome sequencing, gene function annotation analysis and homologous gene related reports showed that TraesKN4A01HG38570 and TraesKN4A01HG38590 were most likely to be candidate genes of qKnps-4A. Phenotypic analysis based on paired near-isogenic lines in the target region showed that qKnps-4A increased KNPS mainly by increasing the number of central florets per spike. We also evaluated the effects of qKnps-4A on other yield-related traits. Moreover, we dissected the QTL cluster of qKnps-4A and qTkw-4A and proved that the phenotypic effects were probably due to close linkage of two or more genes rather than pleiotropic effects of a single gene. This study provides molecular marker resource for wheat molecular breeding designed to improve yield potential, and lay the foundation for gene functional analysis of qKnps-4A.
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Affiliation(s)
- Ran Qin
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Tianhang Ma
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Yibiao Cai
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Xinyao Shi
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Jiajia Cheng
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Jizi Dong
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Chenyang Wang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Shihui Li
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Guoqing Pan
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Yuxiang Guan
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Lei Zhang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Shuang Yang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Huiyuan Xu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Chunhua Zhao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Han Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Ximei Li
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
- Shandong Key Laboratory of Dryland Farming Technology, Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-Tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yongzhen Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
| | - Junming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China.
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
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Amalova A, Yermekbayev K, Griffiths S, Abugalieva S, Babkenov A, Fedorenko E, Abugalieva A, Turuspekov Y. Identification of quantitative trait loci of agronomic traits in bread wheat using a Pamyati Azieva × Paragon mapping population harvested in three regions of Kazakhstan. PeerJ 2022; 10:e14324. [PMID: 36389412 PMCID: PMC9653069 DOI: 10.7717/peerj.14324] [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: 07/27/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
Background Although genome-wide association studies (GWAS) are an increasingly informative tool in the mining of new quantitative trait loci (QTLs), a classical biparental mapping approach is still a powerful, widely used method to search the unique genetic factors associated with important agronomic traits in bread wheat. Methods In this study, a newly constructed mapping population of Pamyati Azieva (Russian Federation) × Paragon (UK), consisting of 94 recombinant inbred lines (RILs), was tested in three different regions of Kazakhstan with the purpose of QTL identification for key agronomic traits. The RILs were tested in 11 environments of two northern breeding stations (Petropavlovsk, North Kazakhstan region, and Shortandy, Aqmola region) and one southeastern station (Almalybak, Almaty region). The following eight agronomic traits were studied: heading days, seed maturation days, plant height, spike length, number of productive spikes, number of kernels per spike, thousand kernel weight, and yield per square meter. The 94 RILs of the PAxP cross were genotyped using Illumina's iSelect 20K single nucleotide polymorphism (SNP) array and resulted in the identification of 4595 polymorphic SNP markers. Results The application of the QTL Cartographer statistical package allowed the identification of 53 stable QTLs for the studied traits. A survey of published studies related to common wheat QTL identification suggested that 28 of those 53 QTLs were presumably novel genetic factors. The SNP markers for the identified QTLs of the analyzed agronomic traits of common wheat can be efficiently applied in ongoing breeding activities in the wheat breeding community using a marker-assisted selection approach.
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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
| | - Kanat Yermekbayev
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan,The John Innes Centre, Norwich, United Kingdom
| | | | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan,Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Adylkhan Babkenov
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Elena Fedorenko
- North Kazakhstan Agricultural Experimental Station, Petropavlovsk, Kazakhstan
| | - Aigul Abugalieva
- Kazakh Research Institute of Agriculture and Plant Industry, Almalybak, Kazakhstan
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan,Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Thirkell TJ, Grimmer M, James L, Pastok D, Allary T, Elliott A, Paveley N, Daniell T, Field KJ. Variation in mycorrhizal growth response among a spring wheat mapping population shows potential to breed for symbiotic benefit. Food Energy Secur 2022; 11:e370. [PMID: 35865673 PMCID: PMC9286679 DOI: 10.1002/fes3.370] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/09/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022] Open
Affiliation(s)
- Tom J. Thirkell
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | | | | | - Daria Pastok
- School of Biology Centre for Plant Sciences University of Leeds Leeds UK
| | - Théa Allary
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | - Ashleigh Elliott
- School of Biology Centre for Plant Sciences University of Leeds Leeds UK
| | | | - Tim Daniell
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | - Katie J. Field
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
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Amalova A, Abugalieva S, Babkenov A, Babkenova S, Turuspekov Y. Genome-wide association study of yield components in spring wheat collection harvested under two water regimes in Northern Kazakhstan. PeerJ 2021; 9:e11857. [PMID: 34395089 PMCID: PMC8323601 DOI: 10.7717/peerj.11857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022] Open
Abstract
Background Bread wheat is the most important cereal in Kazakhstan, where it is grown on over 12 million hectares. One of the major constraints affecting wheat grain yield is drought due to the limited water supply. Hence, the development of drought-resistant cultivars is critical for ensuring food security in this country. Therefore, identifying quantitative trait loci (QTLs) associated with drought tolerance as an essential step in modern breeding activities, which rely on a marker-assisted selection approach. Methods A collection of 179 spring wheat accessions was tested under irrigated and rainfed conditions in Northern Kazakhstan over three years (2018, 2019, and 2020), during which data was collected on nine traits: heading date (HD), seed maturity date (SMD), plant height (PH), peduncle length (PL), number of productive spikes (NPS), spike length (SL), number of kernels per spike (NKS), thousand kernel weight (TKW), and kernels yield per m2 (YM2). The collection was genotyped using a 20,000 (20K) Illumina iSelect SNP array, and 8,662 polymorphic SNP markers were selected for a genome-wide association study (GWAS) to identify QTLs for targeted agronomic traits. Results Out of the total of 237 discovered QTLs, 50 were identified as being stable QTLs for irrigated and rainfed conditions in the Akmola region, Northern Kazakhstan; the identified QTLs were associated with all the studied traits except PH. The results indicate that nine QTLs for HD and 11 QTLs for SMD are presumably novel genetic factors identified in the irrigated and rainfed conditions of Northern Kazakhstan. The identified SNP markers of the QTLs for targeted traits in rainfed conditions can be applied to develop new competitive spring wheat cultivars in arid zones using a marker-assisted selection approach.
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Affiliation(s)
- Akerke Amalova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Saule Abugalieva
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - Adylkhan Babkenov
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Akmola Region, Kazakhstan
| | - Sandukash Babkenova
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Akmola Region, Kazakhstan
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan.,Faculty of Agrobiology, Kazakh National Agrarian University, Almaty, Kazakhstan
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