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Schierenbeck M, Alqudah AM, Thabet SG, Avogadro EG, Dietz JI, Simón MR, Börner A. Natural allelic variation confers diversity in the regulation of flag leaf traits in wheat. Sci Rep 2024; 14:13316. [PMID: 38858489 PMCID: PMC11164900 DOI: 10.1038/s41598-024-64161-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
Flag leaf (FL) dimension has been reported as a key ecophysiological aspect for boosting grain yield in wheat. A worldwide winter wheat panel consisting of 261 accessions was tested to examine the phenotypical variation and identify quantitative trait nucleotides (QTNs) with candidate genes influencing FL morphology. To this end, four FL traits were evaluated during the early milk stage under two growing seasons at the Leibniz Institute of Plant Genetics and Crop Plant Research. The results showed that all leaf traits (Flag leaf length, width, area, and length/width ratio) were significantly influenced by the environments, genotypes, and environments × genotypes interactions. Then, a genome-wide association analysis was performed using 17,093 SNPs that showed 10 novel QTNs that potentially play a role in modulating FL morphology in at least two environments. Further analysis revealed 8 high-confidence candidate genes likely involved in these traits and showing high expression values from flag leaf expansion until its senescence and also during grain development. An important QTN (wsnp_RFL_Contig2177_1500201) was associated with FL width and located inside TraesCS3B02G047300 at chromosome 3B. This gene encodes a major facilitator, sugar transporter-like, and showed the highest expression values among the candidate genes reported, suggesting their positive role in controlling flag leaf and potentially being involved in photosynthetic assimilation. Our study suggests that the detection of novel marker-trait associations and the subsequent elucidation of the genetic mechanism influencing FL morphology would be of interest for improving plant architecture, light capture, and photosynthetic efficiency during grain development.
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Affiliation(s)
- Matías Schierenbeck
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina.
- CONICET CCT La Plata, La Plata, Argentina.
| | - Ahmad Mohammad Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha, Qatar.
| | - Samar Gamal Thabet
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Evangelina Gabriela Avogadro
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Juan Ignacio Dietz
- CONICET CCT La Plata, La Plata, Argentina
- EEA INTA Bordenave, Ruta 76 km 36, Bordenave, Argentina
| | - María Rosa Simón
- Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata, La Plata, Argentina
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
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Zhang W, Chen X, Yang K, Chang S, Zhang X, Liu M, Wu L, Xin M, Hu Z, Liu J, Peng H, Ni Z, Sun Q, Yao Y, Du J. Fine-mapping and validation of the major quantitative trait locus QFlANG-4B for flag leaf angle in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:121. [PMID: 38709317 DOI: 10.1007/s00122-024-04629-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE This study precisely mapped and validated a quantitative trait locus (QTL) located on chromosome 4B for flag leaf angle in wheat. Flag leaf angle (FLANG) is closely related to crop architecture and yield. We previously identified the quantitative trait locus (QTL) QFLANG-4B for FLANG on chromosome 4B, located within a 14-cM interval flanked by the markers Xbarc20 and Xzyh357, using a mapping population of recombinant inbred lines (RILs) derived from a cross between Nongda3331 (ND3331) and Zang1817. In this study, we fine-mapped QFLANG-4B and validated its associated genetic effect. We developed a BC3F3 population using ND3331 as the recurrent parent through marker-assisted selection, as well as near-isogenic lines (NILs) by selfing BC3F3 plants carrying different heterozygous segments for the QFLANG-4B region. We obtained eight recombinant types for QFLANG-4B, narrowing its location down to a 5.3-Mb region. This region contained 76 predicted genes, 7 of which we considered to be likely candidate genes for QFLANG-4B. Marker and phenotypic analyses of individual plants from the secondary mapping populations and their progeny revealed that the FLANG of the ND3331 allele is significantly higher than that of the Zang1817 allele in multiple environments. These results not only provide a basis for the map-based cloning of QFLANG-4B, but also indicate that QFLANG-4B has great potential for marker-assisted selection in wheat breeding programs designed to improve plant architecture and yield.
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Affiliation(s)
- Wenjia Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xinyi Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Kai Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Siyuan Chang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xue Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingde Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Longfei Wu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinkun Du
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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Liu M, Li Z, Kang Y, Lv J, Jin Z, Mu S, Yue H, Li L, Chen P, Li Y. A mutation in CsGME encoding GDP-mannose 3,5-epimerase results in little and wrinkled leaf in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:114. [PMID: 38678513 DOI: 10.1007/s00122-024-04600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/13/2024] [Indexed: 05/01/2024]
Abstract
KEY MESSAGE Map-based cloning revealed that a mutation in a highly conserved amino acid of the CsGME gene encoding GDP-mannose 3,5-epimerase, causes the phenotype of little and wrinkled leaves in cucumbers. Leaf size is a critical determinant of plant architecture in cucumbers, yet only a few genes associated with this trait have been mapped or cloned. Here, we identified and characterized a mutant with little and wrinkled leaves, named lwl-1. Genetic analysis revealed that the phenotype of the lwl-1 was controlled by a single recessive gene. Through map-based cloning, the lwl-1 locus was narrowed down to a 12.22-kb region exclusively containing one fully annotated gene CsGME (CsaV3_2G004170). CsGME encodes GDP-mannose 3,5-epimerase, which is involved in the synthesis of ascorbic acid (ASA) and one of the components of pectin, RG-II. Whole-length sequencing of the 12.22 kb DNA fragment revealed the presence of only a non-synonymous mutation located in the sixth exon of CsGME in lwl-1, resulting in an amino acid alteration from Pro363 to Leu363. This mutation was unique among 118 inbred lines from cucumber natural populations. CsGME expression significantly reduced in various organs of lwl-1, accompanied by a significant decrease in ASA and pectin content in leaves. Both CsGME and Csgme proteins were localized to the cytoplasm. The mutant phenotype exhibited partial recovery after the application of exogenous boric acid. Silencing CsGME in cucumber through VIGS confirmed its role as the causal gene for lwl-1. Transcriptome profiling revealed that CsGME greatly affected the expression of genes related to the cell division process and cell plate formation. This study represents the first report to characterize and clone the CsGME in cucumber, indicating its crucial role in regulating leaf size and development.
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Affiliation(s)
- Mengying Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhaowei Li
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yunfeng Kang
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jinzhao Lv
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhuoshuai Jin
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Siyu Mu
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hongzhong Yue
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
| | - Lixia Li
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Zhang X, Xing P, Lin C, Wang H, Bao Y, Li X. QTL mapping for the flag leaf-related traits using RILs derived from Trititrigia germplasm line SN304 and wheat cultivar Yannong15 in multiple environments. BMC PLANT BIOLOGY 2024; 24:297. [PMID: 38632517 PMCID: PMC11025246 DOI: 10.1186/s12870-024-04993-x] [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: 11/01/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Developing and enriching genetic resources plays important role in the crop improvement. The flag leaf affects plant architecture and contributes to the grain yield of wheat (Triticum aestivum L.). The genetic improvement of flag leaf traits faces problems such as a limited genetic basis. Among the various genetic resources of wheat, Thinopyrum intermedium has been utilized as a valuable resource in genetic improvement due to its disease resistance, large spikes, large leaves, and multiple flowers. In this study, a recombinant inbred line (RIL) population was derived from common wheat Yannong15 and wheat-Th. intermedium introgression line SN304 was used to identify the quantitative trait loci (QTL) for flag leaf-related traits. RESULTS QTL mapping was performed for flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA). A total of 77 QTLs were detected, and among these, 51 QTLs with positive alleles were contributed by SN304. Fourteen major QTLs for flag leaf traits were detected on chromosomes 2B, 3B, 4B, and 2D. Additionally, 28 QTLs and 8 QTLs for flag leaf-related traits were detected in low-phosphorus and drought environments, respectively. Based on major QTLs of positive alleles from SN304, we identified a pair of double-ended anchor primers mapped on chromosome 2B and amplified a specific band of Th. intermedium in SN304. Moreover, there was a major colocated QTL on chromosome 2B, called QFll/Flw/Fla-2B, which was delimited to a physical interval of approximately 2.9 Mb and contained 20 candidate genes. Through gene sequence and expression analysis, four candidate genes associated with flag leaf formation and growth in the QTL interval were identified. CONCLUSION These results promote the fine mapping of QFll/Flw/Fla-2B, which have pleiotropic effects, and will facilitate the identification of candidate genes for flag leaf-related traits. Additionally, this work provides a theoretical basis for the application of Th. intermedium in wheat breeding.
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Affiliation(s)
- Xia Zhang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Piyi Xing
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Caicai Lin
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Honggang Wang
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yinguang Bao
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xingfeng Li
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
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5
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Thakur V, Rane J, Pandey GC, Yadav S. Image facilitated assessment of intra-spike variation in grain size in wheat under high temperature and drought stress. Sci Rep 2023; 13:19850. [PMID: 37963937 PMCID: PMC10645968 DOI: 10.1038/s41598-023-44503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023] Open
Abstract
In wheat (Triticum aestivum L.), the grain size varies according to position within the spike. Exposure to drought and high temperature stress during grain development in wheat reduces grain size, and this reduction also varies across the length of the spike. We developed the phenomics approach involving image-based tools to assess the intra-spike variation in grain size. The grains were arranged corresponding to the spikelet position and the camera of smart phone was used to acquire 333 images. The open-source software ImageJ was used to analyze features of each grain and the image-derived parameters were used to calculate intra-spike variation as standard deviation (ISVAD). The effect of genotype and environment were highly significant on the ISVAD of grain area. Sunstar and Raj 4079 contrasted in the ISVAD of grain area under late sown environment, and RNA sequencing of the spike was done at 25 days after anthesis. The genes for carbohydrate transport and stress response were upregulated in Sunstar as compared to Raj 4079, suggesting that these play a role in intra-spike assimilate distribution. The phenomics method developed may be useful for grain phenotyping and identifying germplasm with low intra-spike variation in grain size for their further validation as parental material in breeding.
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Affiliation(s)
- Vidisha Thakur
- Department of Bioscience & Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan, 304 022, India
| | - Jagadish Rane
- ICAR-Central Institute for Arid Horticulture, Bikaner, Rajasthan, 334006, India.
| | - Girish Chandra Pandey
- Department of Bioscience & Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan, 304 022, India
| | - Satish Yadav
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, Pune, 410 505, India
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Zhao C, Zhou J, Li C, You J, Liu Y, Tang H, Deng M, Xu Q, Zhang Y, Jiang Q, Chen G, Qi P, Jiang Y, Wang J, Li W, Pu Z, Chen G, Jiang Y, Zheng Z, Liu C, Zheng Y, Wei Y, Ma J. A major QTL simultaneously increases the number of spikelets per spike and thousand-kernel weight in a wheat line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:213. [PMID: 37740730 DOI: 10.1007/s00122-023-04459-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023]
Abstract
KEY MESSAGE A novel and stably expressed QTL QSNS.sicau-SSY-7A for spikelet number per spike in wheat without negative effects on thousand-kernel weight was identified and validated in different genetic backgrounds. Spikelet number per spike (SNS) is an important determinant of yield in wheat. In the present study, we combined bulked segregant analysis (BSA) and the wheat 660 K single-nucleotide polymorphism (SNP) array to rapidly identify genomic regions associated with SNS from a recombinant inbred line (RIL) population derived from a cross between the wheat lines S849-8 and SY95-71. A genetic map was constructed using Kompetitive Allele Specific PCR markers in the SNP-enriched region on the long arm of chromosome 7A. A major and stably expressed QTL, QSNS.sicau-SSY-7A, was detected in multiple environments. It was located in a 1.6 cM interval on chromosome arm 7AL flanked by the markers AX-109983514 and AX-109820548. This QTL explained 6.86-15.72% of the phenotypic variance, with LOD values ranging from 3.66 to 8.66. Several genes associated with plant growth and development were identified in the interval where QSNS.sicau-SSY-7A was located on the 'Chinese Spring' wheat and wild emmer reference genomes. Furthermore, the effects of QSNS.sicau-SSY-7A and WHEAT ORTHOLOG OFAPO1(WAPO1) on SNS were analyzed. Interestingly, QSNS.sicau-SSY-7A significantly increased SNS without negative effects on thousand-kernel weight, anthesis date and plant height, demonstrating its great potential for breeding aimed at improving grain yield. Taken together, these results indicate that QSNS.sicau-SSY-7A is a promising locus for yield improvement, and its linkage markers are helpful for fine mapping and molecular breeding.
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Affiliation(s)
- Conghao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jianing You
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy ofAgricultural Sciences, Chengdu, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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7
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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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8
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Wang S, Wang T, Xuan Q, Qu X, Xu Q, Jiang Q, Pu Z, Li Y, Jiang Y, Chen G, Deng M, Liu Y, Tang H, Chen G, He Y, Gou L, Wei Y, Zheng Y, Ma J. Major and stably expressed QTL for traits related to the mature wheat embryo independent of kernel size. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:90. [PMID: 37000252 DOI: 10.1007/s00122-023-04346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Two major and stably expressed QTL for traits related to mature wheat embryo independent of kernel size were identified and validated in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. As the juvenile of a highly differentiated plant, mature wheat (Triticum aestivum L.) embryos are highly significant to agricultural production. To understand the genetic basis of traits related to wheat embryo size, the embryo of mature kernels in a recombination inbred line that contained 126 lines from four environments was measured. The genetic loci of embryo size, including embryo length (EL), embryo width (EW), embryo area (EA), embryo length/kernel length (EL/KL), embryo width/kernel width (EW/KW), and EL/EW, were identified based on a genetic linkage map constructed based on PCR markers and the Wheat 55 K single nucleotide polymorphism (SNP) array. A total of 50 quantitative trait loci (QTL) for traits related to wheat embryo size were detected. Among them, QEL.sicau-2SY-4A for EL and QEW.sicau-2SY-7B for EW were major and stably expressed and were genetically independent of KL and KW, respectively. Their effects were further verified in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. Further analysis showed that TraesCS4A02G343300 and TraesCS7B02G006800 could be candidate genes for QEL.sicau-2SY-4A and QEW.sicau-2SY-7B, respectively. In addition, significant positive correlations between EL and kernel-related traits and the 1,000-grain weight were detected. Collectively, this study broadens our understanding of the genetic basis of wheat embryo size and will be helpful for the further fine-mapping of interesting loci in the future.
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Affiliation(s)
- Surong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tianyu Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qijing Xuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, 621000, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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9
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Niu J, Si Y, Tian S, Liu X, Shi X, Ma S, Yu Z, Ling HQ, Zheng S. A Wheat 660 K SNP array-based high-density genetic map facilitates QTL mapping of flag leaf-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:51. [PMID: 36913011 DOI: 10.1007/s00122-023-04248-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
A high-density genetic map containing 122,620 SNP markers was constructed, which facilitated the identification of eight major flag leaf-related QTL in relatively narrow intervals. The flag leaf plays an important role in photosynthetic capacity and yield potential in wheat. In this study, we used a recombinant inbred line population containing 188 lines derived from a cross between 'Lankao86' (LK86) and 'Ermangmai' to construct a genetic map using the Wheat 660 K single-nucleotide polymorphism (SNP) array. The high-density genetic map contains 122,620 SNP markers spanning 5185.06 cM. It shows good collinearity with the physical map of Chinese Spring and anchors multiple sequences of previously unplaced scaffolds onto chromosomes. Based on the high-density genetic map, we identified seven, twelve, and eight quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), and area (FLA) across eight environments, respectively. Among them, three, one, and four QTL for FLL, FLW, and FLA are major and stably express in more than four environments. The physical distance between the flanking markers for QFll.igdb-3B/QFlw.igdb-3B/QFla.igdb-3B is only 444 kb containing eight high confidence genes. These results suggested that we could directly map the candidate genes in a relatively small region by the high-density genetic map constructed with the Wheat 660 K array. Furthermore, the identification of environmentally stable QTL for flag leaf morphology laid a foundation for the following gene cloning and flag leaf morphology improvement.
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Affiliation(s)
- Jianqing Niu
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, 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, China
| | - Yaoqi Si
- 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, China
| | - Shuiquan Tian
- 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, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- 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, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Shi
- 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, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, 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, China
| | - Zhongqing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Hong-Qing Ling
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, 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, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Shusong Zheng
- 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, China.
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10
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Zanella CM, Rotondo M, McCormick‐Barnes C, Mellers G, Corsi B, Berry S, Ciccone G, Day R, Faralli M, Galle A, Gardner KA, Jacobs J, Ober ES, Sánchez del Rio A, Van Rie J, Lawson T, Cockram J. Longer epidermal cells underlie a quantitative source of variation in wheat flag leaf size. THE NEW PHYTOLOGIST 2023; 237:1558-1573. [PMID: 36519272 PMCID: PMC10107444 DOI: 10.1111/nph.18676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The wheat flag leaf is the main contributor of photosynthetic assimilates to developing grains. Understanding how canopy architecture strategies affect source strength and yield will aid improved crop design. We used an eight-founder population to investigate the genetic architecture of flag leaf area, length, width and angle in European wheat. For the strongest genetic locus identified, we subsequently created a near-isogenic line (NIL) pair for more detailed investigation across seven test environments. Genetic control of traits investigated was highly polygenic, with colocalisation of replicated quantitative trait loci (QTL) for one or more traits identifying 24 loci. For QTL QFll.niab-5A.1 (FLL5A), development of a NIL pair found the FLL5A+ allele commonly conferred a c. 7% increase in flag and second leaf length and a more erect leaf angle, resulting in higher flag and/or second leaf area. Increased FLL5A-mediated flag leaf length was associated with: (1) longer pavement cells and (2) larger stomata at lower density, with a trend for decreased maximum stomatal conductance (Gsmax ) per unit leaf area. For FLL5A, cell size rather than number predominantly determined leaf length. The observed trade-offs between leaf size and stomatal morphology highlight the need for future studies to consider these traits at the whole-leaf level.
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Affiliation(s)
| | - Marilena Rotondo
- NIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
- University of MessinaMessina98122Italy
| | | | | | | | | | - Giulia Ciccone
- NIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
- University of MessinaMessina98122Italy
| | - Rob Day
- NIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | - Michele Faralli
- School of Biological SciencesUniversity of EssexColchesterCO4 3SQUK
| | - Alexander Galle
- BASF Belgium Coordination Center (BBCC) – Innovation Center GhentTechnologiepark‐Zwijnaarde 1019052GhentBelgium
| | | | - John Jacobs
- BASF Belgium Coordination Center (BBCC) – Innovation Center GhentTechnologiepark‐Zwijnaarde 1019052GhentBelgium
| | | | | | - Jeroen Van Rie
- BASF Belgium Coordination Center (BBCC) – Innovation Center GhentTechnologiepark‐Zwijnaarde 1019052GhentBelgium
| | - Tracy Lawson
- School of Biological SciencesUniversity of EssexColchesterCO4 3SQUK
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11
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Kong B, Ma J, Zhang P, Chen T, Liu Y, Che Z, Shahinnia F, Yang D. Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment. BMC Genomics 2023; 24:33. [PMID: 36658498 PMCID: PMC9854125 DOI: 10.1186/s12864-023-09119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Grain yield is a complex and polygenic trait influenced by the photosynthetic source-sink relationship in wheat. The top three leaves, especially the flag leaf, are considered the major sources of photo-assimilates accumulated in the grain. Determination of significant genomic regions and candidate genes affecting flag leaf size can be used in breeding for grain yield improvement. RESULTS With the final purpose of understanding key genomic regions for flag leaf size, a meta-analysis of 521 initial quantitative trait loci (QTLs) from 31 independent QTL mapping studies over the past decades was performed, where 333 loci eventually were refined into 64 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs was 5.28 times less than that of the initial QTLs. Thirty-three MQTLs overlapped the marker trait associations (MTAs) previously reported in genome-wide association studies (GWAS) for flag leaf traits in wheat. A total of 2262 candidate genes for flag leaf size, which were involved in the peroxisome, basal transcription factor, and tyrosine metabolism pathways were identified in MQTL regions by the in silico transcriptome assessment. Of these, the expression analysis of the available genes revealed that 134 genes with > 2 transcripts per million (TPM) were highly and specifically expressed in the leaf. These candidate genes could be critical to affect flag leaf size in wheat. CONCLUSIONS The findings will make further insight into the genetic determinants of flag leaf size and provide some reliable MQTLs and putative candidate genes for the genetic improvement of flag leaf size in wheat.
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Affiliation(s)
- Binxue Kong
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuan Liu
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhuo Che
- Plant Seed Master Station of Gansu Province, Lanzhou, 730000, China
| | - Fahimeh Shahinnia
- Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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12
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Yang J, Liao Z, Du B, Zhang K, Liu L. Two QTL for kernel number per spike identified from durum wheat. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2054728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Jingtian Yang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan, PR China
| | - Zhengqiao Liao
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang, Sichuan, PR China
| | - Baoguo Du
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang, Sichuan, PR China
| | - Kuan Zhang
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang, Sichuan, PR China
| | - Lei Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan, PR China
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang, Sichuan, PR China
- Engineering Research Center for Forest and Grassland Disaster Prevention and Reduction, Mianyang Normal University, Mianyang, Sichuan, PR China
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13
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Lu X, Zhou Z, Wang Y, Wang R, Hao Z, Li M, Zhang D, Yong H, Han J, Wang Z, Weng J, Zhou Y, Li X. Genetic basis of maize kernel protein content revealed by high-density bin mapping using recombinant inbred lines. FRONTIERS IN PLANT SCIENCE 2022; 13:1045854. [PMID: 36589123 PMCID: PMC9798238 DOI: 10.3389/fpls.2022.1045854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Maize with a high kernel protein content (PC) is desirable for human food and livestock fodder. However, improvements in its PC have been hampered by a lack of desirable molecular markers. To identify quantitative trait loci (QTL) and candidate genes for kernel PC, we employed a genotyping-by-sequencing strategy to construct a high-resolution linkage map with 6,433 bin markers for 275 recombinant inbred lines (RILs) derived from a high-PC female Ji846 and low-PC male Ye3189. The total genetic distance covered by the linkage map was 2180.93 cM, and the average distance between adjacent markers was 0.32 cM, with a physical distance of approximately 0.37 Mb. Using this linkage map, 11 QTLs affecting kernel PC were identified, including qPC7 and qPC2-2, which were identified in at least two environments. For the qPC2-2 locus, a marker named IndelPC2-2 was developed with closely linked polymorphisms in both parents, and when tested in 30 high and 30 low PC inbred lines, it showed significant differences (P = 1.9E-03). To identify the candidate genes for this locus, transcriptome sequencing data and PC best linear unbiased estimates (BLUE) for 348 inbred lines were combined, and the expression levels of the four genes were correlated with PC. Among the four genes, Zm00001d002625, which encodes an S-adenosyl-L-methionine-dependent methyltransferase superfamily protein, showed significantly different expression levels between two RIL parents in the endosperm and is speculated to be a potential candidate gene for qPC2-2. This study will contribute to further research on the mechanisms underlying the regulation of maize PC, while also providing a genetic basis for marker-assisted selection in the future.
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Affiliation(s)
- Xin Lu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunhe Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ruiqi Wang
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenhua Wang
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Zhou
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Chen L, Xu Z, Fan X, Zhou Q, Yu Q, Liu X, Liao S, Jiang C, Lin D, Ma F, Feng B, Wang T. Genetic dissection of quantitative trait loci for flag leaf size in bread wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1047899. [PMID: 36600920 PMCID: PMC9807109 DOI: 10.3389/fpls.2022.1047899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Flag leaf size is a crucial trait influencing plant architecture and yield potential in wheat. A recombinant inbred line (RIL) population derived from the cross of W7268 and Chuanyu 12 was employed to identify quantitative trait loci (QTL) controlling flag leaf length (FLL), flag leaf width (FLW), and flag leaf area (FLA) in six environments and the best linear unbiased estimator (BLUE) datasets. Using a 55 K SNP-based genetic map, six major and stable QTL were detected with 6.33-53.12% of explained phenotypic variation. Except for QFlw.cib-4B.3, the other five major QTL were co-located within two intervals on chromosomes 2B and 2D, namely QFll/Fla.cib-2B and QFll/Flw/Fla.cib-2D, respectively. Their interactions and effects on the corresponding traits and yield-related traits were also assessed based on flanking markers. QFll/Fla.cib-2B showed pleiotropic effects on spikelet number per spike (SNS). QFlw.cib-4B.3 and QFll/Flw/Fla.cib-2D had effects on grain number per spike (GNS) and thousand-grain weight (TGW). Comparison analysis suggested that QFll/Fla.cib-2B was likely a new locus. Two candidate genes, TraesCS2B03G0222800 and TraesCS2B03G0230000, associated with leaf development within the interval of QFll/Fla.cib-2B were identified based on expression-pattern analysis, gene annotation, ortholog analysis, and sequence variation. The major QTL and markers reported here provide valuable information for understanding the genetic mechanism underlying flag leaf size as well as breeding utilization in wheat.
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Affiliation(s)
- Liangen Chen
- 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
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qin Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Jiang
- 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
| | - Fang Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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15
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Cseresnyés I, Pokovai K, Bányai J, Mikó P. Root Electrical Capacitance Can Be a Promising Plant Phenotyping Parameter in Wheat. PLANTS (BASEL, SWITZERLAND) 2022; 11:2975. [PMID: 36365428 PMCID: PMC9657365 DOI: 10.3390/plants11212975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
As root electrical capacitance (CR*) was assumed to depend on the stem properties, the efficiency of measuring CR* at flowering for whole-plant phenotyping was assessed in five wheat cultivars in three replicate plots over two years. Linear regression analysis was used to correlate CR* with plant-size parameters and flag-leaf traits (extension and SPAD chlorophyll content) at flowering, and with yield components at maturity. The plot-mean CR* was correlated with the plot leaf area index (LAI), the chlorophyll quantity (LAI×SPAD), and the grain yield across years. At plant scale, CR* was found to show the strongest positive regression with total chlorophyll in the flag leaf (flag leaf area × SPAD; R2: 0.65−0.74) and with grain mass (R2: 0.55−0.70) for each cultivar and year (p < 0.001). Likewise, at plot scale, the regression was strongest between CR* and the LAI×SPAD value (R2: 0.86−0.99; p < 0.01) for the cultivars. Consequently, CR* indicated the total plant nutrient and photosynthate supply at flowering, which depended on root uptake capacity, and strongly influenced the final yield. Our results suggested that the polarization of the active root membrane surfaces was the main contributor to CR*, and that the measurement could be suitable for evaluating root size and functional intensity. In conclusion, the capacitance method can be applied for nondestructive whole-plant phenotyping, with potential to estimate root and shoot traits linked to the nutrient supply, and to predict grain yield. CR* can be incorporated into allometric models of cereal development, contributing to optimal crop management and genetic improvement.
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Affiliation(s)
- Imre Cseresnyés
- Institute for Soil Sciences, Centre for Agricultural Research, ELKH, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Klára Pokovai
- Institute for Soil Sciences, Centre for Agricultural Research, ELKH, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Judit Bányai
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462 Martonvásár, Hungary
| | - Péter Mikó
- Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462 Martonvásár, Hungary
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16
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Du B, Wu J, Islam MS, Sun C, Lu B, Wei P, Liu D, Chen C. Genome-wide meta-analysis of QTL for morphological related traits of flag leaf in bread wheat. PLoS One 2022; 17:e0276602. [PMID: 36279291 PMCID: PMC9591062 DOI: 10.1371/journal.pone.0276602] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022] Open
Abstract
Flag leaf is an important organ for photosynthesis of wheat plants, and a key factor affecting wheat yield. In this study, quantitative trait loci (QTL) for flag leaf morphological traits in wheat reported since 2010 were collected to investigate the genetic mechanism of these traits. Integration of 304 QTLs from various mapping populations into a high-density consensus map composed of various types of molecular markers as well as QTL meta-analysis discovered 55 meta-QTLs (MQTL) controlling morphological traits of flag leaves, of which 10 MQTLs were confirmed by GWAS. Four high-confidence MQTLs (MQTL-1, MQTL-11, MQTL-13, and MQTL-52) were screened out from 55 MQTLs, with an average confidence interval of 0.82 cM and a physical distance of 9.4 Mb, according to the definition of hcMQTL. Ten wheat orthologs from rice (7) and Arabidopsis (3) that regulated leaf angle, development and morphogenesis traits were identified in the hcMQTL region using comparative genomics, and were speculated to be potential candidate genes regulating flag leaf morphological traits in wheat. The results from this study provides valuable information for fine mapping and molecular markers assisted selection to improve morphological characters in wheat flag leaf.
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Affiliation(s)
- Binbin Du
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Jia Wu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Md. Samiul Islam
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Chaoyue Sun
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Baowei Lu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Peipei Wei
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Dong Liu
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Cunwu Chen
- College of Biotechnology and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- * E-mail:
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17
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Wang Y, Qiao L, Yang C, Li X, Zhao J, Wu B, Zheng X, Li P, Zheng J. Identification of genetic loci for flag-leaf-related traits in wheat ( Triticum aestivum L.) and their effects on grain yield. FRONTIERS IN PLANT SCIENCE 2022; 13:990287. [PMID: 36160981 PMCID: PMC9493265 DOI: 10.3389/fpls.2022.990287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Flag-leaf-related traits including length (FLL), width (FLW), area (FLA), thickness (FLT), and volume (FLV) of flag leaves are the most important determinants of plant architecture and yield in wheat. Understanding the genetic basis of these traits could accelerate the breeding of high yield wheat varieties. In this study, we constructed a doubled haploid (DH) population and analyzed flag-leaf-related traits in five experimental locations/years using the wheat 90K single-nucleotide polymorphism array. It's worth noting that a novel method was used to measure FLT and FLV easily. Leaf thickness at two-thirds of the leaf length from tip to collar represented the average leaf thickness as measured with freehand sections and was used to calculate the leaf volume. In addition, flag-leaf-related traits showed positive correlations with yield related traits under two different water regimes. A total of 79 quantitative trait loci (QTL) controlling the five traits were detected among all chromosomes except 4D and 5A, explaining 3.09-14.52% of the phenotypic variation. Among them, 15 stable QTL were identified in more than three environments, including two major QTL for FLT, six for FLW, three for FLA, two for FLT and two for FLV. DH lines with positive alleles at both QTL regions had an average FLL (9.90%), FLW (32.87%), FLT (6.62%), FLA (18.47%), and FLV (20.87%) greater than lines with contrasting alleles. QFLT-2B, QFLV-2A, and QFLV-7D were co-located with yield-related traits. The 15 QTL were validated by tightly linked kompetitive allele specific PCR (KASP) markers in a recombinant inbred line (RIL) population derived from a different cross. QFLL-4A, QFLW-4B, QFLA-5D.1, QFLA-7A, QFLA-7D.1, QFLT-2B, QFLT-6A, QFLV-2A, and QFLV-7D are likely novel loci. These results provide a better understanding of the genetic basis underlying flag-leaf-related traits. Also, target regions for fine mapping and marker-assisted selection were identified and these will be valuable for breeding high yielding bread wheat.
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Affiliation(s)
- Ying Wang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Chenkang Yang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Xiaohua Li
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Pengbo Li
- Institute of Cotton Research, Shanxi Agricultural University, Yuncheng, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
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18
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Wang X, Han B, Sun Y, Kang X, Zhang M, Han H, Zhou S, Liu W, Lu Y, Yang X, Li X, Zhang J, Liu X, Li L. Introgression of chromosome 1P from Agropyron cristatum reduces leaf size and plant height to improve the plant architecture of common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1951-1963. [PMID: 35378599 DOI: 10.1007/s00122-022-04086-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Introducing Agropyron cristatum chromosome 1P into common wheat can significantly reduce the plant height and leaf size, which can improve the plant architecture of common wheat. A new direction in crop breeding is the improvement of plant architecture for dense plantings to obtain higher yields. Wild relatives carry an abundant genetic variation that can increase the diversity of genes for crop genetic improvement. In this study, the A. cristatum 1P addition line, 1PS and 1PL telosomic addition lines were obtained by backcrossing the addition/substitution line II-3-1 (2n = 20'' W + 1P" + 2P") with the commercial recurrent parent cv. Jimai 22. Four continuous years of agronomic trait investigation in the genetic populations suggested that the introduction of A. cristatum chromosome 1P into wheat can significantly improve wheat plant architecture by reducing the plant height, leaf length and leaf width. A. cristatum chromosome arm 1PS reduced the plant height and leaf length of wheat, whereas introducing A. cristatum chromosome arm 1PL reduced the plant height, leaf length and leaf width. Altogether, our results demonstrated that A. cristatum chromosome 1P carries the dominant genes for small leaves and a dwarf habit for the enhancement of plant architecture in wheat. This study highlights wild relative donors as new gene resources for improving wheat plant architecture for dense planting.
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Affiliation(s)
- Xiao Wang
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bohui Han
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yangyang Sun
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xilu Kang
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meng Zhang
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiming Han
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shenghui Zhou
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Liu
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqing Lu
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinming Yang
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuquan Li
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinpeng Zhang
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xu Liu
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Lihui Li
- National Crop Genebank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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19
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Li T, Li Q, Wang J, Yang Z, Tang Y, Su Y, Zhang J, Qiu X, Pu X, Pan Z, Zhang H, Liang J, Liu Z, Li J, Yan W, Yu M, Long H, Wei Y, Deng G. High-resolution detection of quantitative trait loci for seven important yield-related traits in wheat (Triticum aestivum L.) using a high-density SLAF-seq genetic map. BMC Genom Data 2022; 23:37. [PMID: 35562674 PMCID: PMC9107147 DOI: 10.1186/s12863-022-01050-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yield-related traits including thousand grain weight (TGW), grain number per spike (GNS), grain width (GW), grain length (GL), plant height (PH), spike length (SL), and spikelet number per spike (SNS) are greatly associated with grain yield of wheat (Triticum aestivum L.). To detect quantitative trait loci (QTL) associated with them, 193 recombinant inbred lines derived from two elite winter wheat varieties Chuanmai42 and Chuanmai39 were employed to perform QTL mapping in six/eight environments. RESULTS A total of 30 QTLs on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 4A, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified. Among them, six major QTLs QTgw.cib-6A.1, QTgw.cib-6A.2, QGw.cib-6A, QGl.cib-3A, QGl.cib-6A, and QSl.cib-2D explaining 5.96-23.75% of the phenotypic variance were detected in multi-environments and showed strong and stable effects on corresponding traits. Three QTL clusters on chromosomes 2D and 6A containing 10 QTLs were also detected, which showed significant pleiotropic effects on multiple traits. Additionally, three Kompetitive Allele Specific PCR (KASP) markers linked with five of these major QTLs were developed. Candidate genes of QTgw.cib-6A.1/QGl.cib-6A and QGl.cib-3A were analyzed based on the spatiotemporal expression patterns, gene annotation, and orthologous search. CONCLUSIONS Six major QTLs for TGW, GL, GW and SL were detected. Three KASP markers linked with five of these major QTLs were developed. These QTLs and KASP markers will be useful for elucidating the genetic architecture of grain yield and developing new wheat varieties with high and stable yield in wheat.
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Affiliation(s)
- Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Qiao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Juanyu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xvebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Wuyun Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.,State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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20
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Lozada DN, Bosland PW, Barchenger DW, Haghshenas-Jaryani M, Sanogo S, Walker S. Chile Pepper ( Capsicum) Breeding and Improvement in the "Multi-Omics" Era. FRONTIERS IN PLANT SCIENCE 2022; 13:879182. [PMID: 35592583 PMCID: PMC9113053 DOI: 10.3389/fpls.2022.879182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.
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Affiliation(s)
- Dennis N. Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | | | - Mahdi Haghshenas-Jaryani
- Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Stephanie Walker
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States
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21
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TaKLU Plays as a Time Regulator of Leaf Growth via Auxin Signaling. Int J Mol Sci 2022; 23:ijms23084219. [PMID: 35457033 PMCID: PMC9033062 DOI: 10.3390/ijms23084219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
The growth of leaves is subject to strict time regulation. Several genes influencing leaf growth have been identified, but little is known about how genes regulate the orderly initiation and growth of leaves. Here, we demonstrate that TaKLU/TaCYP78A5 contributes to a time regulation mechanism in leaves from initiation to expansion. TaKLU encodes the cytochrome P450 CYP78A5, and its homolog AtKLU has been described whose deletion is detrimental to organ growth. Our results show that TaKLU overexpression increases leaf size and biomass by altering the time of leaf initiation and expansion. TaKLU-overexpressing plants have larger leaves with more cells. Further dynamic observations indicate that enlarged wheat leaves have experienced a longer expansion time. Different from AtKLU inactivation increases leaf number and initiation rates, TaKLU overexpression only smooths the fluctuations of leaf initiation rates by adjusting the initiation time of local leaves, without affecting the overall leaf number and initiation rates. In addition, complementary analyses suggest TaKLU is functionally conserved with AtKLU in controlling the leaf initiation and size and may involve auxin accumulation. Our results provide a new insight into the time regulation mechanisms of leaf growth in wheat.
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22
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Che Y, He Y, Song N, Yang Y, Wei L, Yang X, Zhang Y, Zhang J, Han H, Li X, Zhou S, Liu W, Li L. Four-Year and Five-Developing-Stage Dynamic QTL Mapping for Tiller Number in the Hybrid Population of Agropyron Gaertn. FRONTIERS IN PLANT SCIENCE 2022; 13:835437. [PMID: 35283893 PMCID: PMC8907830 DOI: 10.3389/fpls.2022.835437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Tiller number (TN) is an important agronomic trait affecting gramineous crop yield. To understand the static and dynamic information of quantitative trait locus (QTLs) controlling TN of Agropyron Gaertn., both the unconditional and conditional quantitative trait loci (QTL) mapping of TN were conducted using a cross-pollinated (CP) hybrid population with a total of 113 plant lines from the cross between Agropyron cristatum (L.) Gaertn. Z1842 and Allium mongolicum Keng Z2098, based on the phenotypic data of TN at five developmental stages [i.e., recovering stage (RS), jointing stage (JS), heading stage (HS), flowering stage (FS), and maturity stage (MS)] in 4 years (i.e., 2017, 2018, 2020, and 2021) and the genetic map constructed of 1,023 single-nucleotide polymorphism (SNP) markers. Thirty-seven QTLs controlling TN were detected using two analysis methods in 4 years, which were distributed in six linkage groups. Each QTL explained 2.96-31.11% of the phenotypic variation, with a logarithum of odds (LOD) value of 2.51-13.95. Nine of these loci detected both unconditional and conditional QTLs. Twelve unconditional major QTLs and sixteen conditional major QTLs were detected. Three relatively major stable conditional QTLs, namely, cQTN1-3, cQTN1-5, and cQTN4-1, were expressed in 2020 and 2021. Meantime, two pairs of major QTLs cQTN1-5 and qTN1-4 and also cQTN2-4 and qTN2-3 were located at the same interval but in different years. Except for qTN2-2 and qTN3-5/cQTN3-5, other thirty-four QTLs were first detected in this study. This study provides a better interpretation of genetic factors that selectively control tiller at different developmental stages and a reference for molecular marker-assisted selection in the related plant improvement.
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Affiliation(s)
- Yonghe Che
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yutong He
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Nan Song
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yanping Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Lai Wei
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinpeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiming Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shenghui Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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23
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Nguyen VL, Palmer L, Stangoulis J. Higher Photochemical Quenching and Better Maintenance of Carbon Dioxide Fixation Are Key Traits for Phosphorus Use Efficiency in the Wheat Breeding Line, RAC875. FRONTIERS IN PLANT SCIENCE 2022; 12:816211. [PMID: 35185965 PMCID: PMC8854500 DOI: 10.3389/fpls.2021.816211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Maintaining carbohydrate biosynthesis and C assimilation is critical under phosphorus (P) deficiency as inorganic P (Pi) is essential for ATP synthesis. Low available P in agricultural soils occurs worldwide and fertilizer P sources are being depleted. Thus, identifying biosynthetic traits that are favorable for P use efficiency (PUE) in crops is crucial. This study characterized agronomic traits, gas exchange, and chlorophyll traits of two wheat genotypes that differ in PUE. RAC875 was a P efficient genotype and Wyalkatchem was a P inefficient genotype. The plants were grown in pots under growth room conditions at two P levels; 10 mg P kg-1 soil (low P) and 30 mg P kg-1 soil (adequate P) and gas exchange and chlorophyll fluorescence were measured at the vegetative and booting stages using a portable photosynthesis system (LI-6800, LI-COR, United States). Results showed significant differences in some agronomic traits between the two wheat genotypes, i.e., greater leaf size and area, and a higher ratio of productive tillers to total tillers in RC875 when compared with Wyalkatchem. The CO2 response curve showed Wyalkatchem was more severely affected by low P than RAC875 at the booting stage. The relative ratio of the photosynthetic rate at low P to adequate P was also higher in RAC875 at the booting stage. Photochemical quenching (qP) in RAC875 was significantly higher when compared with Wyalkatchem at the booting stage. Maintaining CO2 fixation capacity under low P and higher qP would be associated with P efficiency in RAC875 and measuring qP could be a potential method to screen for P efficient wheat.
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24
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Li C, Liu H, Wang J, Pan Q, Wang Y, Wu K, Jia P, Mu Y, Tang H, Xu Q, Jiang Q, Liu Y, Qi P, Zhang X, Huang L, Chen G, Wang J, Wei Y, Zheng Y, Gou L, Yao Q, Lan X, Ma J. Characterization and fine mapping of a lesion mimic mutant (Lm5) with enhanced stripe rust and powdery mildew resistance in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:421-438. [PMID: 34661696 DOI: 10.1007/s00122-021-03973-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
A novel light intensity-dependent lesion mimic mutant with enhanced disease resistance was physiologically, biochemically, and genetically characterized, and the causative gene was fine mapped to a 1.28 Mbp interval containing 17 high-confidence genes. Lesion mimic mutants are ideal for studying disease resistance and programmed cell death photosynthesis in plants to improve crop yield. In this study, a novel light intensity-dependent lesion mimic mutant (MC21) was obtained from the wheat variety Chuannong16 (CN16) by ethyl methane sulfonate treatment. The mutant initially developed tiny lesion spots on the basal part of the leaves, which then gradually proceeded down to leaf sheaths, stems, shells, and awns at the flowering stage. The major agronomic traits were significantly altered in the mutant compared to that in the wild-type CN16. Furthermore, the mutant exhibited a lesion phenotype with degenerated chloroplast structure, decreased chlorophyll content, increased level of reactive oxygen species, and increased resistance to stripe rust and powdery mildew. Genetic analysis indicated that the lesion phenotype was controlled by a novel single semi-dominant nuclear gene. The target gene was mapped on chromosome arm 2AL located between Kompetitive Allele Specific PCR (KASP) markers, KASP-4211 and KASP-5353, and tentatively termed as lesion mimic 5 (Lm5). The fine mapping suggested that Lm5 was located in a 1.28 Mbp interval between markers KASP-5825 and KASP-9366; 17 high-confidence candidate genes were included in this genomic region. This study provides an important foundational step for further cloning of Lm5 using a map-based approach.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qi Pan
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yue Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kunyan Wu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peiying Jia
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaojun Zhang
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lulu Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qifu Yao
- College of Agroforestry Engineering and Planning/Guizhou Key Laboratory of Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, 554300, China.
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Forero-Junco LM, Alanin KWS, Djurhuus AM, Kot W, Gobbi A, Hansen LH. Bacteriophages Roam the Wheat Phyllosphere. Viruses 2022; 14:v14020244. [PMID: 35215838 PMCID: PMC8876510 DOI: 10.3390/v14020244] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/13/2022] Open
Abstract
The phyllosphere microbiome plays an important role in plant fitness. Recently, bacteriophages have been shown to play a role in shaping the bacterial community composition of the phyllosphere. However, no studies on the diversity and abundance of phyllosphere bacteriophage communities have been carried out until now. In this study, we extracted, sequenced, and characterized the dsDNA and ssDNA viral community from a phyllosphere for the first time. We sampled leaves from winter wheat (Triticum aestivum), where we identified a total of 876 virus operational taxonomic units (vOTUs), mostly predicted to be bacteriophages with a lytic lifestyle. Remarkably, 848 of these vOTUs corresponded to new viral species, and we estimated a minimum of 2.0 × 106 viral particles per leaf. These results suggest that the wheat phyllosphere harbors a large and active community of novel bacterial viruses. Phylloviruses have potential applications as biocontrol agents against phytopathogenic bacteria or as microbiome modulators to increase plant growth-promoting bacteria.
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Affiliation(s)
- Laura Milena Forero-Junco
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Correspondence: (L.M.F.-J.); (L.H.H.)
| | - Katrine Wacenius Skov Alanin
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark
| | - Amaru Miranda Djurhuus
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (K.W.S.A.); (A.M.D.); (W.K.); (A.G.)
- Correspondence: (L.M.F.-J.); (L.H.H.)
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26
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Lozada DN, Nunez G, Lujan P, Dura S, Coon D, Barchenger DW, Sanogo S, Bosland PW. Genomic regions and candidate genes linked with Phytophthora capsici root rot resistance in chile pepper (Capsicum annuum L.). BMC PLANT BIOLOGY 2021; 21:601. [PMID: 34922461 PMCID: PMC8684135 DOI: 10.1186/s12870-021-03387-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/07/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Phytophthora root rot, caused by Phytophthora capsici, is a major disease affecting Capsicum production worldwide. A recombinant inbred line (RIL) population derived from the hybridization between 'Criollo de Morellos-334' (CM-334), a resistant landrace from Mexico, and 'Early Jalapeno', a susceptible cultivar was genotyped using genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers. A GBS-SNP based genetic linkage map for the RIL population was constructed. Quantitative trait loci (QTL) mapping dissected the genetic architecture of P. capsici resistance and candidate genes linked to resistance for this important disease were identified. RESULTS Development of a genetic linkage map using 1,973 GBS-derived polymorphic SNP markers identified 12 linkage groups corresponding to the 12 chromosomes of chile pepper, with a total length of 1,277.7 cM and a marker density of 1.5 SNP/cM. The maximum gaps between consecutive SNP markers ranged between 1.9 (LG7) and 13.5 cM (LG5). Collinearity between genetic and physical positions of markers reached a maximum of 0.92 for LG8. QTL mapping identified genomic regions associated with P. capsici resistance in chromosomes P5, P8, and P9 that explained between 19.7 and 30.4% of phenotypic variation for resistance. Additive interactions between QTL in chromosomes P5 and P8 were observed. The role of chromosome P5 as major genomic region containing P. capsici resistance QTL was established. Through candidate gene analysis, biological functions associated with response to pathogen infections, regulation of cyclin-dependent protein serine/threonine kinase activity, and epigenetic mechanisms such as DNA methylation were identified. CONCLUSIONS Results support the genetic complexity of the P. capsici-Capsicum pathosystem and the possible role of epigenetics in conferring resistance to Phytophthora root rot. Significant genomic regions and candidate genes associated with disease response and gene regulatory activity were identified which allows for a deeper understanding of the genomic landscape of Phytophthora root rot resistance in chile pepper.
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Affiliation(s)
- Dennis N Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Guillermo Nunez
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Phillip Lujan
- Extension Plant Sciences, Plant Diagnostic Clinic, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Srijana Dura
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Danise Coon
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Paul W Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA
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Chen S, Liu F, Wu W, Jiang Y, Zhan K. A SNP-based GWAS and functional haplotype-based GWAS of flag leaf-related traits and their influence on the yield of bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3895-3909. [PMID: 34436627 DOI: 10.1007/s00122-021-03935-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
The genetic architecture of five flag leaf morphology traits was dissected by the functional haplotype-based GWAS and a standard SNP-based GWAS in a diverse population consisting of 197 varieties. Flag leaf morphology (FLM) is a critical factor affecting plant architecture and grain yield in wheat. The genetic architecture of FLM traits has been extensively studied with QTL mapping in bi-parental populations, while few studies exploited genome-wide association studies (GWAS) in diverse populations. In this study, a panel of 197 elite and historical varieties from China was evaluated for five FLM traits including the length (FLL), width (FLW), ratio (FLR), area (FLA) and angle (FLANG) as well as yield in nine environments. Based on the phenotypic correlation between yield and FLL (-0.43), FLA (- 0.32) and FLW (0.11), an empirical FLM index combining the three FLM traits proved to be a good predictor for yield. Two GWAS approaches were applied to dissect the genetic architecture of five FLM traits with a Wheat660K SNP array. The functional haplotype-based GWAS revealed 6, 5 and 7 QTL for FLANG, FLL and FLR, respectively, whereas two QTL for FLW and one for FLR were identified by the standard SNP-based GWAS. Due to co-localization, there were 18 independent QTL and 10 of them were close to known ones. One co-localized QTL on chromosome 5A was associated with FLL, FLANG and FLR. Moreover, both GWAS approaches identified a novel QTL for FLR on chromosome 6B which was not reported in previous studies. This study provides new insights into the relationship between FLM and yield and broadens our understanding of the genetic architecture of FLM traits in wheat.
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Affiliation(s)
- Shulin Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Wenxue Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Kehui Zhan
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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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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Blanc E, Barbillon P, Fournier C, Lecarpentier C, Pradal C, Enjalbert J. Functional-Structural Plant Modeling Highlights How Diversity in Leaf Dimensions and Tillering Capability Could Promote the Efficiency of Wheat Cultivar Mixtures. FRONTIERS IN PLANT SCIENCE 2021; 12:734056. [PMID: 34659301 PMCID: PMC8511389 DOI: 10.3389/fpls.2021.734056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 06/02/2023]
Abstract
Increasing the cultivated diversity has been identified as a major leverage for the agroecological transition as it can help improve the resilience of low input cropping systems. For wheat, which is the most cultivated crop worldwide in terms of harvested area, the use of cultivar mixtures is spreading in several countries, but studies have seldom focused on establishing mixing rules based on plant architecture. Yet, the aerial architecture of plants and the overall canopy structure are critical for field performance as they greatly influence light interception, plant interactions and yield. The very high number of trait combinations in wheat mixtures makes it difficult to conduct experimentations on this issue, which is why a modeling approach appears to be an appropriate solution. In this study, we used WALTer, a functional structural plant model (FSPM), to simulate wheat cultivar mixtures and try to better understand how differences between cultivars in key traits of the aerial architecture influence mixture performance. We simulated balanced binary mixtures of cultivars differing for different critical plant traits: final height, leaf dimensions, leaf insertion angle and tillering capability. Our study highlights the impact of the leaf dimensions and the tillering capability on the performance of the simulated mixtures, which suggests that traits impacting the plants' leaf area index (LAI) have more influence on the performance of the stand than traits impacting the arrangement of the leaves. Our results show that the performance of mixtures is very variable depending on the values of the explored architectural traits. In particular, the best performances were achieved by mixing cultivars with different leaf dimensions and different tillering capability, which is in agreement with numerous studies linking the diversity of functional traits in plant communities to their productivity. However, some of the worst performances were also achieved by mixing varieties differing in their aerial architecture, which suggests that diversity is not a sufficient criterion to design efficient mixtures. Overall, these results highlight the importance of simulation-based explorations for establishing assembly rules to design efficient mixtures.
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Affiliation(s)
- Emmanuelle Blanc
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France
| | - Pierre Barbillon
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | | | | | - Christophe Pradal
- CIRAD, UMR AGAP Institut, Montpellier, France
- INRIA and LIRMM, Univ Montpellier, CNRS, Montpellier, France
| | - Jérôme Enjalbert
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France
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30
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Zhang S, Yu Z, Qi X, Wang Z, Zheng Y, Ren H, Liang S, Zheng X. Construction of a High-Density Genetic Map and Identification of Leaf Trait-Related QTLs in Chinese Bayberry ( Myrica rubra). FRONTIERS IN PLANT SCIENCE 2021; 12:675855. [PMID: 34194452 PMCID: PMC8238045 DOI: 10.3389/fpls.2021.675855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Chinese bayberry (Myrica rubra) is an economically important fruit tree that is grown in southern China. Owing to its over 10-year seedling period, the crossbreeding of bayberry is challenging. The characteristics of plant leaves are among the primary factors that control plant architecture and potential yields, making the analysis of leaf trait-related genetic factors crucial to the hybrid breeding of any plant. In the present study, molecular markers associated with leaf traits were identified via a whole-genome re-sequencing approach, and a genetic map was thereby constructed. In total, this effort yielded 902.11 Gb of raw data that led to the identification of 2,242,353 single nucleotide polymorphisms (SNPs) in 140 F1 individuals and parents (Myrica rubra cv. Biqizhong × Myrica rubra cv. 2012LXRM). The final genetic map ultimately incorporated 31,431 SNPs in eight linkage groups, spanning 1,351.85 cM. This map was then used to assemble and update previous scaffold genomic data at the chromosomal level. The genome size of M. rubra was thereby established to be 275.37 Mb, with 94.98% of sequences being assembled into eight pseudo-chromosomes. Additionally, 18 quantitative trait loci (QTLs) associated with nine leaf and growth-related traits were identified. Two QTL clusters were detected (the LG3 and LG5 clusters). Functional annotations further suggested two chlorophyll content-related candidate genes being identified in the LG5 cluster. Overall, this is the first study on the QTL mapping and identification of loci responsible for the regulation of leaf traits in M. rubra, offering an invaluable scientific for future marker-assisted selection breeding and candidate gene analyses.
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Affiliation(s)
| | | | - Xingjiang Qi
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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31
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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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Muhammad A, Li J, Hu W, Yu J, Khan SU, Khan MHU, Xie G, Wang J, Wang L. Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models. Sci Rep 2021; 11:6767. [PMID: 33762669 PMCID: PMC7990932 DOI: 10.1038/s41598-021-86127-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023] Open
Abstract
Wheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.
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Affiliation(s)
- Ali Muhammad
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Agriculture, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jianguo Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weichen Hu
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Yu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, 311300, China
| | - Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guosheng Xie
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jibin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China.
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
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Sheng C, Song S, Zhou R, Li D, Gao Y, Cui X, Tang X, Zhang Y, Tu J, Zhang X, Wang L. QTL-Seq and Transcriptome Analysis Disclose Major QTL and Candidate Genes Controlling Leaf Size in Sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:580846. [PMID: 33719280 PMCID: PMC7943740 DOI: 10.3389/fpls.2021.580846] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Leaf size is a crucial component of sesame (Sesamum indicum L.) plant architecture and further influences yield potential. Despite that it is well known that leaf size traits are quantitative traits controlled by large numbers of genes, quantitative trait loci (QTL) and candidate genes for sesame leaf size remain poorly understood. In the present study, we combined the QTL-seq approach and SSR marker mapping to identify the candidate genomic regions harboring QTL controlling leaf size traits in an RIL population derived from a cross between sesame varieties Zhongzhi No. 13 (with big leaves) and ZZM2289 (with small leaves). The QTL mapping revealed 56 QTL with phenotypic variation explained (PVE) from 1.87 to 27.50% for the length and width of leaves at the 1/3 and 1/2 positions of plant height. qLS15-1, a major and environmentally stable pleiotropic locus for both leaf length and width explaining 5.81 to 27.50% phenotypic variation, was located on LG15 within a 408-Kb physical genomic region flanked by the markers ZMM6185 and ZMM6206. In this region, a combination of transcriptome analysis with gene annotations revealed three candidate genes SIN_1004875, SIN_1004882, and SIN_1004883 associated with leaf growth and development in sesame. These findings provided insight into the genetic characteristics and variability for sesame leaf and set up the foundation for future genomic studies on sesame leaves and will serve as gene resources for improvement of sesame plant architecture.
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Affiliation(s)
- Chen Sheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Shengnan Song
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yuan Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xianghua Cui
- Zhumadian Academy of Agricultural Sciences, Zhumadian, China
| | - Xuehui Tang
- Xiangyang Academy of Agricultural Sciences, Xiangyang, China
| | - Yanxin Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, China
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
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Mo Z, Zhu J, Wei J, Zhou J, Xu Q, Tang H, Mu Y, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Li W, Wei Y, Zheng Y, Lan X, Ma J. The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat ( Triticum turgidum L.) Population: Chinese Landrace "Ailanmai" × Wild Emmer. FRONTIERS IN PLANT SCIENCE 2021; 12:732837. [PMID: 34531890 PMCID: PMC8439258 DOI: 10.3389/fpls.2021.732837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/18/2021] [Indexed: 05/08/2023]
Abstract
Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace "Ailanmai" × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.
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Affiliation(s)
- Ziqiang Mo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiatai Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Xiujin Lan
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Jian Ma
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35
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Tu Y, Liu H, Liu J, Tang H, Mu Y, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Pu Z, Chen G, Peng Y, Jiang Y, Xu Q, Kang H, Lan X, Wei Y, Zheng Y, Ma J. QTL mapping and validation of bread wheat flag leaf morphology across multiple environments in different genetic backgrounds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:261-278. [PMID: 33026461 DOI: 10.1007/s00122-020-03695-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/22/2020] [Indexed: 05/24/2023]
Abstract
Eight major and stably expressed QTL for flag leaf morphology across eleven environments were identified and validated using newly developed KASP markers in seven biparental populations with different genetic backgrounds. Flag leaf morphology is a determinant trait influencing plant architecture and yield potential in wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population with a 55 K SNP-based constructed genetic map was used to map quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), area (FLA), angle (FLANG), opening angle (FLOA), and bend angle (FLBA) in eleven environments. Eight major QTL were detected in 11 environments with 5.73-54.38% of explained phenotypic variation. These QTL were successfully verified using the newly developed Kompetitive Allele Specific PCR (KASP) markers in six biparental populations with different genetic backgrounds. Among these 8 major QTL, two co-located intervals were identified. Significant interactions for both FLL- and FLW-related QTL were detected. Comparison analysis showed that QFll.sau-SY-2B and QFla.sau-SY-2B are likely new loci. Significant relationships between flag leaf- and yield-related traits were observed and discussed. Several genes associated with leaf development including the ortholog of maize ZmRAVL1, a B3-domain transcription factor involved in regulation of leaf angle, were predicted in physical intervals harboring these major QTL on reference genomes of bread wheat 'Chinese spring', T. turgidum, and Aegilops tauschii. Taken together, these results broaden our understanding on genetic basis of flag leaf morphology and provide clues for fine mapping and marker-assisted breeding wheat with optimized plant architecture for promising loci.
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Affiliation(s)
- Yang Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Qu X, Liu J, Xie X, Xu Q, Tang H, Mu Y, Pu Z, Li Y, Ma J, Gao Y, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Habib A, Wei Y, Zheng Y, Lan X, Ma J. Genetic Mapping and Validation of Loci for Kernel-Related Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:667493. [PMID: 34163507 PMCID: PMC8215603 DOI: 10.3389/fpls.2021.667493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 05/11/2023]
Abstract
Kernel size (KS) and kernel weight play a key role in wheat yield. Phenotypic data from six environments and a Wheat55K single-nucleotide polymorphism array-based constructed genetic linkage map from a recombinant inbred line population derived from the cross between the wheat line 20828 and the line SY95-71 were used to identify quantitative trait locus (QTL) for kernel length (KL), kernel width (KW), kernel thickness (KT), thousand-kernel weight (TKW), kernel length-width ratio (LWR), KS, and factor form density (FFD). The results showed that 65 QTLs associated with kernel traits were detected, of which the major QTLs QKL.sicau-2SY-1B, QKW.sicau-2SY-6D, QKT.sicau-2SY-2D, and QTKW.sicau-2SY-2D, QLWR.sicau-2SY-6D, QKS.sicau-2SY-1B/2D/6D, and QFFD.sicau-2SY-2D controlling KL, KW, KT, TKW, LWR, KS, and FFD, and identified in multiple environments, respectively. They were located on chromosomes 1BL, 2DL, and 6DS and formed three QTL clusters. Comparison of genetic and physical interval suggested that only QKL.sicau-2SY-1B located on chromosome 1BL was likely a novel QTL. A Kompetitive Allele Specific Polymerase chain reaction (KASP) marker, KASP-AX-109379070, closely linked to this novel QTL was developed and used to successfully confirm its effect in two different genetic populations and three variety panels consisting of 272 Chinese wheat landraces, 300 Chinese wheat cultivars most from the Yellow and Huai River Valley wheat region, and 165 Sichuan wheat cultivars. The relationships between kernel traits and other agronomic traits were detected and discussed. A few predicted genes involved in regulation of kernel growth and development were identified in the intervals of these identified major QTL. Taken together, these stable and major QTLs provide valuable information for understanding the genetic composition of kernel yield and provide the basis for molecular marker-assisted breeding.
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Affiliation(s)
- Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinlin Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Xiujin Lan,
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Jian Ma, ;
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37
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Li C, Tang H, Luo W, Zhang X, Mu Y, Deng M, Liu Y, Jiang Q, Chen G, Wang J, Qi P, Pu Z, Jiang Y, Wei Y, Zheng Y, Lan X, Ma J. A novel, validated, and plant height-independent QTL for spike extension length is associated with yield-related traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3381-3393. [PMID: 32870326 DOI: 10.1007/s00122-020-03675-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/21/2020] [Indexed: 05/24/2023]
Abstract
A novel, stably expressed, and plant height-independent QTL for spike extension length on 5AS was identified and validated in different populations using a newly developed and tightly linked KASP marker. As an important component of plant height (PH), spike extension length (SEL) plays a significant role in formation of an ideotype in wheat. Despite the fact that numerous loci for SEL in wheat have been reported, our knowledge on PH-independent loci remains to be limited. In this study, two recombinant inbred line (RIL) populations genotyped using the Wheat55K SNP were used to detect quantitative trait loci (QTL) controlling SEL across six environments. A total of 30 QTL for SEL were detected in these two RIL populations, and four of them, i.e., QSEL.sicau-2CN-4D, QSEL.sicau-2SY-4B.2, QSEL.sicau-2SY-4D.1, and QSEL.sicau-2CN-5A, were stably expressed. Genetic and conditional QTL analysis showed that the first three were significantly associated with PH, while the last one, QSEL.sicau-2CN-5A, is independent of PH. Comparison of genetic and physical maps suggested that only QSEL.sicau-2CN-5A located on chromosome arm 5AS is likely a novel QTL. A Kompetitive Allele-Specific PCR (KASP) marker, KASP-AX-110413733, tightly linked to this novel QTL was developed to successfully confirm its effect in three different genetic populations. Further, in the interval where QSEL.sicau-2CN-5A was located on 'Chinese Spring' wheat reference genome, three promising genes mainly expressed in wheat stem were predicated and they all encode the cytochrome P450 that was demonstrated to be closely associated with SEL elongation in rice. In addition, significant correlations between SEL and PH, spikelet number per spike, and thousand-grain weight were also detected. Altogether, our results broaden our understanding on genetic basis of SEL and will be useful for marker-based selection of lines with different SELs and fine mapping the novel and PH-independent QTL QSEL.sicau-2CN-5A.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuemei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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38
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Jin J, Liu D, Qi Y, Ma J, Zhen W. Major QTL for Seven Yield-Related Traits in Common Wheat (Triticum aestivum L.). Front Genet 2020; 11:1012. [PMID: 33005181 PMCID: PMC7485215 DOI: 10.3389/fgene.2020.01012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 08/10/2020] [Indexed: 11/13/2022] Open
Abstract
Flag leaves, plant height (PH), and spike-related traits are key determinants contributing to yield potential in wheat. In this study, we developed a recombinant inbred line (RIL) population with 94 lines derived from the cross between 'AS985472' and 'Sumai 3.' A genetic map spanned 3553.69 cM in length were constructed using 1978 DArT markers. Severn traits including flag leaf width (FLW), flag leaf length (FLL), PH, anthesis date (AD), spike length (SL), spikelet number spike (SNS), and spike density (SD) were evaluated against this RIL population under three different environments. Combined phenotypic data and genetic map, we identified quantitative trait loci (QTL) for each trait. A total of four major and stably expressed QTLs for FLW, PH, and SD were detected on chromosomes 2D and 4B. Of them, the major QTLs individually explained 10.10 - 30.68% of the phenotypic variation. QTLs with pleiotropic effects were identified on chromosomes 4A and 6D as well. Furthermore, the genetic relationships between seven yield-related traits were detected and discussed. A few genes related to leaf growth and development at the interval of a major locus for FLW on chromosome 2D were predicated. Overall, the present study provided useful information for understanding the genetic basis of yield-related traits and will be useful for marker-assisted selection in wheat breeding.
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Affiliation(s)
- Jingjing Jin
- College of Plant Protection, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Dan Liu
- Neijiang Academy of Agricultural Sciences, Neijiang, China.,School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Yongzhi Qi
- College of Plant Protection, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wenchao Zhen
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Agronomy, Hebei Agricultural University, Baoding, China
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39
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Liu J, Tang H, Qu X, Liu H, Li C, Tu Y, Li S, Habib A, Mu Y, Dai S, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Chen G, Li W, Jiang Y, Wei Y, Lan X, Zheng Y, Ma J. A novel, major, and validated QTL for the effective tiller number located on chromosome arm 1BL in bread wheat. PLANT MOLECULAR BIOLOGY 2020; 104:173-185. [PMID: 32734417 DOI: 10.1007/s11103-020-01035-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/09/2020] [Indexed: 05/24/2023]
Abstract
A novel and major QTL for the effective tiller number was identified on chromosomal arm 1BL and validated in two genetic backgrounds The effective tiller number (ETN) substantially influences plant architecture and the wheat yield improvement. In this study, we constructed a genetic map of the 2SY (20828/SY95-71) recombinant inbred line population based on the Wheat 55K array as well as the simple sequence repeat (SSR) and Kompetitive Allele Specific PCR (KASP) markers. A comparison between the genetic and physical maps indicated the marker positions were consistent in the two maps. Additionally, we identified seven tillering-related quantitative trait locus (QTLs), including Qetn-sau-1B.1, which is a major QTL localized to a 6.17-cM interval flanked by markers AX-89635557 and AX-111544678 on chromosome 1BL. The Qetn-sau-1B.1 QTL was detected in eight environments and explained 12.12-55.71% of the phenotypic variance. Three genes associated with the ETN were detected in the physical interval of Qetn-sau-1B.1. We used a tightly linked KASP marker, KASP-AX-110129912, to further validate this QTL in two other populations with different genetic backgrounds. The results indicated that Qetn-sau-1B.1 significantly increased the ETN by up to 23.5%. The results of this study will be useful for the precise mapping and cloning of Qetn-sau-1B.1.
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Affiliation(s)
- Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuiqing Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shoufeng Dai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Abstract
Wheat was one of the first grain crops domesticated by humans and remains among the major contributors to the global calorie and protein budget. The rapidly expanding world population demands further enhancement of yield and performance of wheat. Phenotypic information has historically been instrumental in wheat breeding for improved traits. In the last two decades, a steadily growing collection of tools and imaging software have given us the ability to quantify shoot, root, and seed traits with progressively increasing accuracy and throughput. This review discusses challenges and advancements in image analysis platforms for wheat phenotyping at the organ level. Perspectives on how these collective phenotypes can inform basic research on understanding wheat physiology and breeding for wheat improvement are also provided.
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