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Li Y, Hu J, Lin H, Qiu D, Qu Y, Du J, Hou L, Ma L, Wu Q, Liu Z, Zhou Y, Li H. Mapping QTLs for adult-plant resistance to powdery mildew and stripe rust using a recombinant inbred line population derived from cross Qingxinmai × 041133. FRONTIERS IN PLANT SCIENCE 2024; 15:1397274. [PMID: 38779062 PMCID: PMC11109386 DOI: 10.3389/fpls.2024.1397274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
A recombinant inbred line (RIL) population derived from wheat landrace Qingxinmai and breeding line 041133 exhibited segregation in resistance to powdery mildew and stripe rust in five and three field tests, respectively. A 16K genotyping by target sequencing (GBTS) single-nucleotide polymorphism (SNP) array-based genetic linkage map was used to dissect the quantitative trait loci (QTLs) for disease resistance. Four and seven QTLs were identified for adult-plant resistance (APR) against powdery mildew and stripe rust. QPm.caas-1B and QPm.caas-5A on chromosomes 1B and 5A were responsible for the APR against powdery mildew in line 041133. QYr.caas-1B, QYr.caas-3B, QYr.caas-4B, QYr.caas-6B.1, QYr.caas-6B.2, and QYr.caas-7B detected on the five B-genome chromosomes of line 041133 conferred its APR to stripe rust. QPm.caas-1B and QYr.caas.1B were co-localized with the pleiotropic locus Lr46/Yr29/Sr58/Pm39/Ltn2. A Kompetitive Allele Specific Polymorphic (KASP) marker KASP_1B_668028290 was developed to trace QPm/Yr.caas.1B. Four lines pyramiding six major disease resistance loci, PmQ, Yr041133, QPm/Yr.caas-1B, QPm.caas-2B.1, QYr.caas-3B, and QPm.caas-6B, were developed. They displayed effective resistance against both powdery mildew and stripe rust at the seedling and adult-plant stages.
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Affiliation(s)
- Yahui Li
- College of Life and Environmental Science, Minzu University of China, Beijing, China
| | - Jinghuang Hu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huailong Lin
- Jiushenghe Seed Industry Co. Ltd., Changji, China
| | - Dan Qiu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yunfeng Qu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiuyuan Du
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Lu Hou
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University/Key Laboratory of Agricultural Integrated Pest Management, Xining, China
| | - Lin Ma
- Datong Hui and Tu Autonomous County Agricultural Technology Extension Center, Xining, China
| | - Qiuhong Wu
- Institute of Biotechnology, Xianghu Laboratory, Hangzhou, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yijun Zhou
- College of Life and Environmental Science, Minzu University of China, Beijing, China
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Biotechnology, Xianghu Laboratory, Hangzhou, China
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Huang S, Zhang Y, Ren H, Zhang X, Yu R, Liu S, Zeng Q, Wang Q, Yuan F, Singh RP, Bhavani S, Wu J, Han D, Kang Z. High density mapping of wheat stripe rust resistance gene QYrXN3517-1BL using QTL mapping, BSE-Seq and candidate gene analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:39. [PMID: 36897402 DOI: 10.1007/s00122-023-04282-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/21/2022] [Indexed: 06/18/2023]
Abstract
Fine mapping of a major stripe rust resistance locus QYrXN3517-1BL to a 336 kb region that includes 12 candidate genes. Utilization of genetic resistance is an effective strategy to control stripe rust disease in wheat. Cultivar XINONG-3517 (XN3517) has remained highly resistant to stripe rust since its release in 2008. To understand the genetic architecture of stripe rust resistance, Avocet S (AvS) × XN3517 F6 RIL population was assessed for stripe rust severity in five field environments. The parents and RILs were genotyped by using the GenoBaits Wheat 16 K Panel. Four stable QTL from XINONG-3517 were detected on chromosome arms 1BL, 2AL, 2BL, and 6BS, named as QYrXN3517-1BL, QYrXN3517-2AL, QYrXN3517-2BL, and QYrXN3517-6BS, respectively. Based on the Wheat 660 K array and bulked segregant exome sequencing (BSE-Seq), the most effective QTL on chromosome 1BL is most likely different from the known adult plant resistance gene Yr29 and was mapped to a 1.7 cM region [336 kb, including twelve candidate genes in International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 1.0]. The 6BS QTL was identified as Yr78, and the 2AL QTL was probably same as QYr.caas-2AL or QYrqin.nwafu-2AL. The novel QTL on 2BL was effective in seedling stage against the races used in phenotyping. In addition, allele-specifc quantitative PCR (AQP) marker nwafu.a5 was developed for QYrXN3517-1BL to assist marker-assisted breeding.
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Affiliation(s)
- Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yibo Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Hui Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Rui Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237, Texcoco, Estado de Mexico, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56237, Texcoco, Estado de Mexico, Mexico
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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Pang Y, Liu C, Lin M, Ni F, Li W, Cai J, Zhang Z, Zhu H, Liu J, Wu J, Bai G, Liu S. Mapping QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Landrace. Int J Mol Sci 2022; 23:ijms23179662. [PMID: 36077059 PMCID: PMC9456275 DOI: 10.3390/ijms23179662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Wheat stripe (yellow) rust is a worldwide disease that seriously reduces wheat grain yield and quality. Adult-plant resistance (APR) to stripe rust is generally more durable but usually controlled by multiple genes with partial resistance. In this study, a recombinant inbred line population was developed from a cross between a Chinese wheat landrace, Tutoumai, with APR to stripe rust, and a highly susceptible wheat cultivar, Siyang 936. The population was genotyped by genotyping-by-sequencing and phenotyped for APR to stripe rust in four consecutive field experiments. Three QTLs, QYr.sdau-1BL, QYr.sdau-5BL, and QYr.sdau-6BL, were identified for APR to stripe rust, and explained 8.0–21.2%, 10.1–22.7%, and 11.6–18.0% of the phenotypic variation, respectively. QYr.sdau-1BL was further mapped to a 21.6 Mb region using KASP markers derived from SNPs identified by RNA-seq of the two parents. In the QYr.sdau-1BL region, 13 disease-resistance-related genes were differently expressed between the two parents, and therefore were considered as the putative candidates of QYr.sdau-1BL. This study provides favorable gene/QTL and high-throughput markers to breeding programs for marker-assisted selection of the wheat stripe rust APR genes.
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Affiliation(s)
- Yunlong Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Chunxia Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Meng Lin
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Fei Ni
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Wenhui Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jin Cai
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Ziliang Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Huaqiang Zhu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jingxian Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Shubing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China
- Correspondence:
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Muhammad A, Hu W, Li Z, Li J, Xie G, Wang J, Wang L. Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS. Int J Mol Sci 2020; 21:ijms21165649. [PMID: 32781752 PMCID: PMC7460857 DOI: 10.3390/ijms21165649] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.
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Affiliation(s)
- Ali Muhammad
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Weicheng Hu
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Zhaoyang Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Jianguo Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
| | - Guosheng Xie
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
| | - Jibin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
- Correspondence: (J.W.); (L.W.)
| | - Lingqiang Wang
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan 430070, China; (A.M.); (W.H.); (Z.L.); (J.L.); (G.X.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning 530004, China
- Correspondence: (J.W.); (L.W.)
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Kumar D, Kumar A, Chhokar V, Gangwar OP, Bhardwaj SC, Sivasamy M, Prasad SVS, Prakasha TL, Khan H, Singh R, Sharma P, Sheoran S, Iquebal MA, Jaiswal S, Angadi UB, Singh G, Rai A, Singh GP, Kumar D, Tiwari R. Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:748. [PMID: 32582265 PMCID: PMC7286347 DOI: 10.3389/fpls.2020.00748] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 05/20/2023]
Abstract
Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.
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Affiliation(s)
- Deepender Kumar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Animesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Vinod Chhokar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | - M. Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | - S. V. Sai Prasad
- ICAR-Indian Agricultural Research Institute, Regional Station, Indore, India
| | - T. L. Prakasha
- ICAR-Indian Agricultural Research Institute, Regional Station, Indore, India
| | - Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa B. Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
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