1
|
Blancon J, Buet C, Dubreuil P, Tixier MH, Baret F, Praud S. Maize green leaf area index dynamics: genetic basis of a new secondary trait for grain yield in optimal and drought conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:68. [PMID: 38441678 PMCID: PMC10914915 DOI: 10.1007/s00122-024-04572-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/03/2024] [Indexed: 03/07/2024]
Abstract
KEY MESSAGE Green Leaf Area Index dynamics is a promising secondary trait for grain yield and drought tolerance. Multivariate GWAS is particularly well suited to identify the genetic determinants of the green leaf area index dynamics. Improvement of maize grain yield is impeded by important genotype-environment interactions, especially under drought conditions. The use of secondary traits, that are correlated with yield, more heritable and less prone to genotype-environment interactions, can increase breeding efficiency. Here, we studied the genetic basis of a new secondary trait: the green leaf area index (GLAI) dynamics over the maize life cycle. For this, we used an unmanned aerial vehicle to characterize the GLAI dynamics of a diverse panel in well-watered and water-deficient trials in two years. From the dynamics, we derived 24 traits (slopes, durations, areas under the curve), and showed that six of them were heritable traits representative of the panel diversity. To identify the genetic determinants of GLAI, we compared two genome-wide association approaches: a univariate (single-trait) method and a multivariate (multi-trait) method combining GLAI traits, grain yield, and precocity. The explicit modeling of correlation structure between secondary traits and grain yield in the multivariate mixed model led to 2.5 times more associations detected. A total of 475 quantitative trait loci (QTLs) were detected. The genetic architecture of GLAI traits appears less complex than that of yield with stronger-effect QTLs that are more stable between environments. We also showed that a subset of GLAI QTLs explains nearly one fifth of yield variability across a larger environmental network of 11 water-deficient trials. GLAI dynamics is a promising grain yield secondary trait in optimal and drought conditions, and the detected QTLs could help to increase breeding efficiency through a marker-assisted approach.
Collapse
Affiliation(s)
- Justin Blancon
- UMR GDEC, INRAE, Université Clermont Auvergne, 63000, Clermont-Ferrand, France.
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France.
| | - Clément Buet
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France
| | - Pierre Dubreuil
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France
| | | | | | - Sébastien Praud
- Biogemma, Centre de Recherche de Chappes, 63720, Chappes, France
| |
Collapse
|
2
|
Lu X, Liu P, Tu L, Guo X, Wang A, Zhu Y, Jiang Y, Zhang C, Xu Y, Chen Z, Wu X. Joint-GWAS, Linkage Mapping, and Transcriptome Analysis to Reveal the Genetic Basis of Plant Architecture-Related Traits in Maize. Int J Mol Sci 2024; 25:2694. [PMID: 38473942 DOI: 10.3390/ijms25052694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/04/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Plant architecture is one of the key factors affecting maize yield formation and can be divided into secondary traits, such as plant height (PH), ear height (EH), and leaf number (LN). It is a viable approach for exploiting genetic resources to improve plant density. In this study, one natural panel of 226 inbred lines and 150 family lines derived from the offspring of T32 crossed with Qi319 were genotyped by using the MaizeSNP50 chip and the genotyping by sequence (GBS) method and phenotyped under three different environments. Based on the results, a genome-wide association study (GWAS) and linkage mapping were analyzed by using the MLM and ICIM models, respectively. The results showed that 120 QTNs (quantitative trait nucleotides) and 32 QTL (quantitative trait loci) related to plant architecture were identified, including four QTL and 40 QTNs of PH, eight QTL and 41 QTNs of EH, and 20 QTL and 39 QTNs of LN. One dominant QTL, qLN7-2, was identified in the Zhangye environment. Six QTNs were commonly identified to be related to PH, EH, and LN in different environments. The candidate gene analysis revealed that Zm00001d021574 was involved in regulating plant architecture traits through the autophagy pathway, and Zm00001d044730 was predicted to interact with the male sterility-related gene ms26. These results provide abundant genetic resources for improving maize plant architecture traits by using approaches to biological breeding.
Collapse
Affiliation(s)
- Xuefeng Lu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Region, Guiyang 550006, China
| | - Pengfei Liu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Liang Tu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Xiangyang Guo
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Angui Wang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yunfang Zhu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yulin Jiang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Region, Guiyang 550006, China
| | - Chunlan Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Yan Xu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Zehui Chen
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Xun Wu
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Ministry of Agriculture and Rural Affairs Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Region, Guiyang 550006, China
| |
Collapse
|
3
|
Wen T, Zhang X, Zhu J, Zhang S, Rhaman MS, Zeng W. A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1338086. [PMID: 38384753 PMCID: PMC10880447 DOI: 10.3389/fpls.2024.1338086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
The leaf scorching trait at flowering is a crucial thermosensitive phenotype in maize under high temperature stress (HS), yet the genetic basis of this trait remains poorly understood. In this study, we genotyped a 254 RIL-F2:8 population, derived from the leaf scorch-free parental inbred line Abe2 and the leaf scorching maternal inbred line B73, using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 10,112 polymorphic SLAF markers were developed, and a high-density genetic map with a total length of 1,475.88 cM was constructed. The average sequencing depth of the parents was 55.23X, and that of the progeny was 12.53X. Then, we identified a total of 16 QTLs associated with thermotolerant traits at flowering, of which four QTLs of leaf scorching damage (LS) were distributed on chromosomes 1 (qLS1), 2 (qLS2.1, qLS2.2) and 3 (qLS3), which could explain 19.73% of phenotypic variation. Combining one qLS1 locus with QTL-seq results led to the identification of 6 candidate genes. Expression experiments and sequence variation indicated that Zm00001d033328, encoding N-acetyl-gamma-glutamyl-phosphate reductase, was the most likely candidate gene controlling thermotolerant traits at flowering. In summary, the high-density genetic map and genetic basis of thermotolerant traits lay a critical foundation for mapping other complex traits and identifying the genes associated with thermotolerant traits in maize.
Collapse
Affiliation(s)
- Tingting Wen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
- Seed Administration Station of Shandong Province, Jinan, China
| | - Xuefei Zhang
- Taian Daiyue District Bureau of Agriculture and Rural Affairs, Taian, China
| | - Jiaojiao Zhu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Susu Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Wei Zeng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| |
Collapse
|
4
|
Karnatam KS, Mythri B, Un Nisa W, Sharma H, Meena TK, Rana P, Vikal Y, Gowda M, Dhillon BS, Sandhu S. Silage maize as a potent candidate for sustainable animal husbandry development-perspectives and strategies for genetic enhancement. Front Genet 2023; 14:1150132. [PMID: 37303948 PMCID: PMC10250641 DOI: 10.3389/fgene.2023.1150132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Maize is recognized as the queen of cereals, with an ability to adapt to diverse agroecologies (from 58oN to 55oS latitude) and the highest genetic yield potential among cereals. Under contemporary conditions of global climate change, C4 maize crops offer resilience and sustainability to ensure food, nutritional security, and farmer livelihood. In the northwestern plains of India, maize is an important alternative to paddy for crop diversification in the wake of depleting water resources, reduced farm diversity, nutrient mining, and environmental pollution due to paddy straw burning. Owing to its quick growth, high biomass, good palatability, and absence of anti-nutritional components, maize is also one of the most nutritious non-legume green fodders. It is a high-energy, low-protein forage commonly used for dairy animals like cows and buffalos, often in combination with a complementary high-protein forage such as alfalfa. Maize is also preferred for silage over other fodders due to its softness, high starch content, and sufficient soluble sugars required for proper ensiling. With a rapid population increase in developing countries like China and India, there is an upsurge in meat consumption and, hence, the requirement for animal feed, which entails high usage of maize. The global maize silage market is projected to grow at a compound annual growth rate of 7.84% from 2021 to 2030. Factors such as increasing demand for sustainable and environment-friendly food sources coupled with rising health awareness are fueling this growth. With the dairy sector growing at about 4%-5% and the increasing shortage faced for fodder, demand for silage maize is expected to increase worldwide. The progress in improved mechanization for the provision of silage maize, reduced labor demand, lack of moisture-related marketing issues as associated with grain maize, early vacancy of farms for next crops, and easy and economical form of feed to sustain household dairy sector make maize silage a profitable venture. However, sustaining the profitability of this enterprise requires the development of hybrids specific for silage production. Little attention has yet been paid to breeding for a plant ideotype for silage with specific consideration of traits such as dry matter yield, nutrient yield, energy in organic matter, genetic architecture of cell wall components determining their digestibility, stalk standability, maturity span, and losses during ensiling. This review explores the available information on the underlying genetic mechanisms and gene/gene families impacting silage yield and quality. The trade-offs between yield and nutritive value in relation to crop duration are also discussed. Based on available genetic information on inheritance and molecular aspects, breeding strategies are proposed to develop maize ideotypes for silage for the development of sustainable animal husbandry.
Collapse
Affiliation(s)
- Krishna Sai Karnatam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Bikkasani Mythri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Wajhat Un Nisa
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Heena Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Tarun Kumar Meena
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Prabhat Rana
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - M. Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Baldev Singh Dhillon
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Surinder Sandhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| |
Collapse
|
5
|
Du F, Tao Y, Ma C, Zhu M, Guo C, Xu M. Effects of the quantitative trait locus qPss3 on inhibition of photoperiod sensitivity and resistance to stalk rot disease in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:126. [PMID: 37165143 DOI: 10.1007/s00122-023-04370-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE We identified a quantitative trait locus, qPss3, and fine-mapped the causal locus to a 120-kb interval in maize. This locus inhibits the photoperiod sensitivity caused by ZmCCT9 and ZmCCT10, resulting in earlier flowering by 2 ~ 4 days without reduction in stalk-rot resistance in certain genotypes. Photoperiod sensitivity is a key factor affecting the adaptation of maize (Zea mays L.) to high-latitude growing areas. Although many genes associated with flowering time have been identified in maize, no gene that inhibits photoperiod sensitivity has been reported. In our previous study, we detected large differences in photoperiod sensitivity among maize inbred lines with the same photoperiod-sensitive allele at the ZmCCT10 locus. Here, we used two segregating populations with the same genetic backgrounds but different ZmCCT10 alleles to perform quantitative trait locus (QTL) analysis. We identified a unique QTL, qPss3, on chromosome 3 in the population carrying the sensitive ZmCCT10 allele. After sequential fine-mapping, we eventually delimited qPss3 to an interval of ~ 120 kb. qPss3 behaved as a dominant locus and caused earlier flowering by 2-4 days via inhibiting ZmCCT10-induced photoperiod sensitivity under long-day conditions. qPss3 also inhibited the photoperiod sensitivity induced by another flowering-related gene, ZmCCT9. For application in agriculture, an F1 hybrid heterozygous at both qPss3 and ZmCCT10 loci constitutes an optimal allele combination, showing high resistance to stalk rot without a significant delay in flowering time. Moreover, qPss3 is of great value in regulating the flowering time of tropical maize grown at high-latitude regions.
Collapse
Affiliation(s)
- Feili Du
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Yiyuan Tao
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Chuanyu Ma
- Research Pipeline Enablement SBC, Syngenta Biotechnology China Co. Ltd., Beijing, China
| | - Mang Zhu
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Chenyu Guo
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Mingliang Xu
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China.
| |
Collapse
|
6
|
Khaipho-Burch M, Ferebee T, Giri A, Ramstein G, Monier B, Yi E, Romay MC, Buckler ES. Elucidating the patterns of pleiotropy and its biological relevance in maize. PLoS Genet 2023; 19:e1010664. [PMID: 36943844 PMCID: PMC10030035 DOI: 10.1371/journal.pgen.1010664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/09/2023] [Indexed: 03/23/2023] Open
Abstract
Pleiotropy-when a single gene controls two or more seemingly unrelated traits-has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56-32.3% of intervals show some degree of pleiotropy. We then assess the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide and large effect variants, leaving the prevalence of detectable pleiotropy relatively low.
Collapse
Affiliation(s)
| | - Taylor Ferebee
- Department of Computational Biology, Cornell University, Ithaca, New York
| | - Anju Giri
- Institute for Genomic Diversity, Cornell University, Ithaca, New York
| | - Guillaume Ramstein
- Institute for Genomic Diversity, Cornell University, Ithaca, New York
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Brandon Monier
- Institute for Genomic Diversity, Cornell University, Ithaca, New York
| | - Emily Yi
- Institute for Genomic Diversity, Cornell University, Ithaca, New York
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York
- Institute for Genomic Diversity, Cornell University, Ithaca, New York
- USDA-ARS, Ithaca, New York, United States of America
| |
Collapse
|
7
|
Zhang M, Chen Y, Xing H, Ke W, Shi Y, Sui Z, Xu R, Gao L, Guo G, Li J, Xing J, Zhang Y. Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:772-790. [PMID: 36354146 DOI: 10.1111/jipb.13408] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.
Collapse
Affiliation(s)
- Ming Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yanhong Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Agronomy College of Shandong Agricultural University, Taian, 271018, China
| | - Hongyan Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yunlu Shi
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhipeng Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Yantai Science and Technology Innovation Promotion Center, Yantai, 264003, China
| | - Ruibin Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Ganggang Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Germplasm Resources and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
8
|
Xu H, Ming B, Wang K, Xue J, Hou P, Li S, Xie R. The effects of photoperiod and temperature-related factors on maize leaf number and leaf positional distribution in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1006245. [PMID: 36844043 PMCID: PMC9950512 DOI: 10.3389/fpls.2023.1006245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Quantifying the effects of various environmental conditions on maize leaf number is essential to understanding the environmental adaptations and population structure of maize plants and for enhancing maize productivity. In this study, seeds of three temperate-adapted maize cultivars, each belonging to different maturity classes, were sown on eight different dates. Sowing dates ranged from the middle of April to early July, which allowed us to cover a wide range of environmental conditions. Random forest regression and multiple regression models with variance partitioning analyses were used to assess the effects of environmental factors on the number of leaves and their distributions on maize primary stems. We demonstrated that the total leaf number (TLN) increased in the three cultivars in the following order: FK139 < JNK728 < ZD958, and variations in TLN for each cultivar were 1.5, 1.76, and 2.75 leaves, respectively. The variation in TLN was ascribed to changes in LB (leaf number below the primary ear), which were higher than variations in LA (leaf number above the primary ear). Variations in TLN and LB were mainly affected by the photoperiod during growth stages V7 to V11, and differences in TLN and LB in response to different photoperiods ranged from 1.34 to 2.95 leaves h-l. Variations in LA was mainly affected by temperature-related factors. Therefore, the results of this study enhanced our current understanding of key environmental conditions that affect maize leaf numbers, and provides scientific support for the benefits of adjusting sowing dates and selecting suitable cultivars to mitigate the effects of climate change on maize production.
Collapse
Affiliation(s)
| | | | | | | | | | - Shaokun Li
- *Correspondence: Shaokun Li, ; Ruizhi Xie,
| | - Ruizhi Xie
- *Correspondence: Shaokun Li, ; Ruizhi Xie,
| |
Collapse
|
9
|
Feng C, Zou S, Zhang J. Genetic architecture of microhabitat adaptation traits in a pair of sympatric Primulina species. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2023.2176169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Affiliation(s)
- Chen Feng
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
| | - Shuaiyu Zou
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
| | - Jie Zhang
- Jiangxi Provincial Key Laboratory of ex situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, PR China
| |
Collapse
|
10
|
Dai W, Yu H, Liu K, Chengxu Y, Yan J, Zhang C, Xi N, Liu H, Xiangchen C, Zou C, Zhang M, Gao S, Pan G, Ma L, Shen Y. Combined linkage mapping and association analysis uncovers candidate genes for 25 leaf-related traits across three environments in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:12. [PMID: 36662253 DOI: 10.1007/s00122-023-04285-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Combined linkage and association analysis revealed five co-localized genetic loci across multiple environments. The key gene Zm00001d026491 was further verified to influence leaf length by candidate gene association analysis. Leaf morphology and number determine the canopy structure and thus affect crop yield. Herein, the genetic basis and key genes for 25 leaf-related traits, including leaf lengths (LL), leaf widths (LW), and leaf areas (LA) of eight continuous leaves under the tassel, and the number of leaves above the primary ear (LAE), were dissected by using an association panel and a biparental population. Using an intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, 290 quantitative trait loci (QTL) controlling these traits were detected across different locations, among which 115 QTL were individually repeatedly identified in at least two environments. Using the association panel, 165 unique significant single-nucleotide polymorphisms (SNPs) were associated with target traits (P < 2.15E-06), of which 35 were separately detected across multiple environments. In total, 42 pleiotropic QTL/SNPs (pQTL/SNPs) were responsible for at least two of the LL, LW, LA, and LAE traits across multiple environments. Combining the QTL mapping and association study, five unique SNPs were located within the confidence intervals of seven QTL, and 77 genes were identified based on the linkage disequilibrium regions of co-localized SNP loci. Gene-based association studies verified that the intragenic variants in the candidate gene Zm00001d026491 influenced LL of the third leaf counted from the top node. These findings will provide vital information to understanding the genetic basis of leaf-related traits and help to cultivate maize varieties with ideal plant architecture.
Collapse
Affiliation(s)
- Wei Dai
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hong Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujuan Chengxu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaquan Yan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Na Xi
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoyang Xiangchen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minyan Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|
11
|
Li B, Wang Z, Jiang H, Luo JH, Guo T, Tian F, Rossi V, He Y. ZmCCT10-relayed photoperiod sensitivity regulates natural variation in the arithmetical formation of male germinal cells in maize. THE NEW PHYTOLOGIST 2023; 237:585-600. [PMID: 36266961 DOI: 10.1111/nph.18559] [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: 08/13/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Extensive mutational screening studies have documented genes regulating anther and pollen development. Knowledge concerning how formation of male germinal cell is arithmetically controlled in natural populations, under different environmental conditions, is lacking. We counted pollen number within a single anther and a maize-teosinte BC2 S3 recombinant inbred line population to identify ZmCCT10 as a major determinant of pollen number variation. ZmCCT10 was originally identified as a photoperiod-sensitive negative regulator of flowering. ZmCCT10 inactivation, after transposon insertion within its promoter, is proposed to have accelerated maize spread toward higher latitudes, thus allowing temperate maize to flower under long-day conditions. We showed that the active ZmCCT10 allele decreased pollen formation. As different active and inactive ZmCCT10 alleles have been found in natural maize populations, this represents the first report of a gene controlling pollen number in a crop natural population. These findings suggest that higher pollen number, which provides a competitive advantage in open-pollinated populations, may have been one of the major driving forces for the selection of an inactive ZmCCT10 allele during tropical maize domestication. We provide evidence that ZmCCT10 has opposite effects on cell proliferation of archesporial and tapetum cells and it modulates expression of key regulators during early anther development.
Collapse
Affiliation(s)
- Bo Li
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Zi Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Huan Jiang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Jin-Hong Luo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Ting Guo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Feng Tian
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Vincenzo Rossi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Bergamo, 24126, Italy
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| |
Collapse
|
12
|
Rivas JG, Gutierrez AV, Defacio RA, Schimpf J, Vicario AL, Hopp HE, Paniego NB, Lia VV. Morphological and genetic diversity of maize landraces along an altitudinal gradient in the Southern Andes. PLoS One 2022; 17:e0271424. [PMID: 36542628 PMCID: PMC9770441 DOI: 10.1371/journal.pone.0271424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Maize (Zea mays ssp. mays) is a major cereal crop worldwide and is traditionally or commercially cultivated almost all over the Americas. The North-Western Argentina (NWA) region constitutes one of the main diversity hotspots of the Southern Andes, with contrasting landscapes and a large number of landraces. Despite the extensive collections performed by the "Banco Activo de Germoplasma INTA Pergamino, Argentina" (BAP), most of them have not been characterized yet. Here we report the morphological and molecular evaluation of 30 accessions collected from NWA, along an altitudinal gradient between 1120 and 2950 meters above sea level (masl). Assessment of morphological variation in a common garden allowed the discrimination of two groups, which differed mainly in endosperm type and overall plant size. Although the groups retrieved by the molecular analyses were not consistent with morphological clusters, they showed a clear pattern of altitudinal structuring. Affinities among accessions were not in accordance with racial assignments. Overall, our results revealed that there are two maize gene pools co-existing in NWA, probably resulting from various waves of maize introduction in pre-Columbian times as well as from the adoption of modern varieties by local farmers. In conclusion, the NWA maize landraces preserved at the BAP possess high morphological and molecular variability. Our results highlight their potential as a source of diversity for increasing the genetic basis of breeding programs and provide useful information to guide future sampling and conservation efforts.
Collapse
Affiliation(s)
- Juan Gabriel Rivas
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Angela Veronica Gutierrez
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Raquel Alicia Defacio
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Pergamino, Buenos Aires, Argentina
| | - Jorge Schimpf
- Facultad de Ciencias Agrarias, Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Ana Laura Vicario
- Laboratorio de Marcadores Moleculares y Fitopatología, Instituto Nacional de Semillas, (INASE), Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norma Beatriz Paniego
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Veronica Viviana Lia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
| |
Collapse
|
13
|
Busche M, Hake S, Brunkard JO. Terminal ear 1 and phytochromes B1/B2 regulate maize leaf initiation independently. Genetics 2022; 223:6887217. [PMID: 36495288 PMCID: PMC9910401 DOI: 10.1093/genetics/iyac182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Higher plants generate new leaves from shoot meristems throughout their vegetative lifespan. The tempo of leaf initiation is dynamically regulated by physiological cues, but little is known about the underlying genetic signaling pathways that coordinate this rate. Two maize (Zea mays) mutants, terminal ear1 (te1) and phytochrome B1;phytochrome B2 (phyB1;phyB2), oppositely affect leaf initiation rates and total leaf number at the flowering time: te1 mutants make leaves faster whereas phyB1;phyB2 mutants make leaves slower than wild-type plants. To test whether PhyB1, PhyB2, and TE1 act in overlapping or distinct pathways to regulate leaf initiation, we crossed te1 and phyB1;phyB2 created an F2 population segregating for these three mutations and quantified various phenotypes among the resulting genotypes, including leaf number, leaf initiation rate, plant height, leaf length, leaf width, number of juvenile leaves, stalk diameter, and dry shoot biomass. Leaf number and initiation rate in phyB1;phyB2;te1 plants fell between the extremes of the two parents, suggesting an additive genetic interaction between te1 and phyB1;phyB2 rather than epistasis. Therefore, we conclude that PhyB1, PhyB2, and TE1 likely control leaf initiation through distinct signaling pathways.
Collapse
Affiliation(s)
- Michael Busche
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Sarah Hake
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA,Plant Gene Expression Center, USDA Agricultural Research Service, Albany, CA 94710, USA
| | - Jacob O Brunkard
- Corresponding author: Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53715, USA.
| |
Collapse
|
14
|
Vishal MK, Saluja R, Aggrawal D, Banerjee B, Raju D, Kumar S, Chinnusamy V, Sahoo RN, Adinarayana J. Leaf Count Aided Novel Framework for Rice ( Oryza sativa L.) Genotypes Discrimination in Phenomics: Leveraging Computer Vision and Deep Learning Applications. PLANTS (BASEL, SWITZERLAND) 2022; 11:2663. [PMID: 36235529 PMCID: PMC9614605 DOI: 10.3390/plants11192663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/02/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Drought is a detrimental factor to gaining higher yields in rice (Oryza sativa L.), especially amid the rising occurrence of drought across the globe. To combat this situation, it is essential to develop novel drought-resilient varieties. Therefore, screening of drought-adaptive genotypes is required with high precision and high throughput. In contemporary emerging science, high throughput plant phenotyping (HTPP) is a crucial technology that attempts to break the bottleneck of traditional phenotyping. In traditional phenotyping, screening significant genotypes is a tedious task and prone to human error while measuring various plant traits. In contrast, owing to the potential advantage of HTPP over traditional phenotyping, image-based traits, also known as i-traits, were used in our study to discriminate 110 genotypes grown for genome-wide association study experiments under controlled (well-watered), and drought-stress (limited water) conditions, under a phenomics experiment in a controlled environment with RGB images. Our proposed framework non-destructively estimated drought-adaptive plant traits from the images, such as the number of leaves, convex hull, plant-aspect ratio (plant spread), and similarly associated geometrical and morphological traits for analyzing and discriminating genotypes. The results showed that a single trait, the number of leaves, can also be used for discriminating genotypes. This critical drought-adaptive trait was associated with plant size, architecture, and biomass. In this work, the number of leaves and other characteristics were estimated non-destructively from top view images of the rice plant for each genotype. The estimation of the number of leaves for each rice plant was conducted with the deep learning model, YOLO (You Only Look Once). The leaves were counted by detecting corresponding visible leaf tips in the rice plant. The detection accuracy was 86-92% for dense to moderate spread large plants, and 98% for sparse spread small plants. With this framework, the susceptible genotypes (MTU1010, PUSA-1121 and similar genotypes) and drought-resistant genotypes (Heera, Anjali, Dular and similar genotypes) were grouped in the core set with a respective group of drought-susceptible and drought-tolerant genotypes based on the number of leaves, and the leaves' emergence during the peak drought-stress period. Moreover, it was found that the number of leaves was significantly associated with other pertinent morphological, physiological and geometrical traits. Other geometrical traits were measured from the RGB images with the help of computer vision.
Collapse
Affiliation(s)
| | - Rohit Saluja
- CSE, Indian Institute of Technology Bombay, Mumbai 400076, India
- Indian Institute of Information Technology, Hyderabad 500032, India
| | | | - Biplab Banerjee
- CSRE, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Dhandapani Raju
- Indian Council of Agricultural Research—Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Sudhir Kumar
- Indian Council of Agricultural Research—Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Viswanathan Chinnusamy
- Indian Council of Agricultural Research—Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Rabi Narayan Sahoo
- Indian Council of Agricultural Research—Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | | |
Collapse
|
15
|
Shi J, Wang Y, Wang C, Wang L, Zeng W, Han G, Qiu C, Wang T, Tao Z, Wang K, Huang S, Yu S, Wang W, Chen H, Chen C, He C, Wang H, Zhu P, Hu Y, Zhang X, Xie C, Lu X, Li P. Linkage mapping combined with GWAS revealed the genetic structural relationship and candidate genes of maize flowering time-related traits. BMC PLANT BIOLOGY 2022; 22:328. [PMID: 35799118 PMCID: PMC9264602 DOI: 10.1186/s12870-022-03711-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Flowering time is an important agronomic trait of crops and significantly affects plant adaptation and seed production. Flowering time varies greatly among maize (Zea mays) inbred lines, but the genetic basis of this variation is not well understood. Here, we report the comprehensive genetic architecture of six flowering time-related traits using a recombinant inbred line (RIL) population obtained from a cross between two maize genotypes, B73 and Abe2, and combined with genome-wide association studies to identify candidate genes that affect flowering time. RESULTS Our results indicate that these six traits showed extensive phenotypic variation and high heritability in the RIL population. The flowering time of this RIL population showed little correlation with the leaf number under different environmental conditions. A genetic linkage map was constructed by 10,114 polymorphic markers covering the whole maize genome, which was applied to QTL mapping for these traits, and identified a total of 82 QTLs that contain 13 flowering genes. Furthermore, a combined genome-wide association study and linkage mapping analysis revealed 17 new candidate genes associated with flowering time. CONCLUSIONS In the present study, by using genetic mapping and GWAS approaches with the RIL population, we revealed a list of genomic regions and candidate genes that were significantly associated with flowering time. This work provides an important resource for the breeding of flowering time traits in maize.
Collapse
Affiliation(s)
- Jian Shi
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yunhe Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chuanhong Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Lei Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Zeng
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Guomin Han
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chunhong Qiu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Tengyue Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Tao
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Kaiji Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shijie Huang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shuaishuai Yu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wanyi Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hongyi Chen
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chen Chen
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chen He
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hui Wang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Peiling Zhu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Yuanyuan Hu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Xin Zhang
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Chuanxiao Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Xiaoduo Lu
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| | - Peijin Li
- The National Engineering Laboratory of Crop Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
| |
Collapse
|
16
|
Abraham-Juárez MJ, Barnes AC, Aragón-Raygoza A, Tyson D, Kur A, Strable J, Rellán-Álvarez R. The arches and spandrels of maize domestication, adaptation, and improvement. CURRENT OPINION IN PLANT BIOLOGY 2021; 64:102124. [PMID: 34715472 DOI: 10.1016/j.pbi.2021.102124] [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: 04/06/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland - a member of the Pueblo of Laguna tribe of New Mexico - wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop.
Collapse
Affiliation(s)
- María Jazmín Abraham-Juárez
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, 36821, Mexico
| | - Allison C Barnes
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alejandro Aragón-Raygoza
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA; Unidad de Genómica Avanzada, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Guanajuato, Mexico
| | - Destiny Tyson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Andi Kur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Josh Strable
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Rubén Rellán-Álvarez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
| |
Collapse
|
17
|
Dong MY, Lei L, Fan XW, Li YZ. Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes. AOB PLANTS 2021; 13:plab048. [PMID: 34567492 PMCID: PMC8459886 DOI: 10.1093/aobpla/plab048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Flowering in maize (Zea mays) is influenced by photoperiod. The CO, CO-like/COL and TOC1 (CCT) domain protein-encoding genes in maize, ZmCCTs, are particularly important for photoperiod sensitivity. However, little is known about CCT protein-encoding gene number across plant species or among maize inbred lines. Therefore, we analysed CCT protein-encoding gene number across plant species, and characterized ZmCCTs in different inbred lines, including structural variations (SVs), copy number variations (CNVs), expression under stresses, dark-dark (DD) and dark-light (DL) cycles, interaction network and associations with maize quantitative trait loci (QTLs) by referring to the latest v4 genome data of B73. Gene number varied greatly across plant species, more in polyploids than in diploids. The numbers of ZmCCTs identified were 58 in B73, 59 in W22, 48 in Mo17, and 57 in Huangzao4 for temperate maize inbred lines, and 68 in tropical maize inbred line SK. Some ZmCCTs underwent duplications and presented chromosome collinearity. Structural variations and CNVs were found but they had no germplasm specificity. Forty-two ZmCCTs responded to stresses. Expression of 37 ZmCCTs in embryonic leaves during seed germination of maize under DD and DL cycles was roughly divided into five patterns of uphill pattern, downhill-pattern, zigzag-pattern, └-pattern and ⅃-pattern, indicating some of them have a potential to perceive dark and/or dark-light transition. Thirty-three ZmCCTs were co-expressed with 218 other maize genes; and 24 ZmCCTs were associated with known QTLs. The data presented in this study will help inform further functions of ZmCCTs.
Collapse
Affiliation(s)
- Ming-You Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - Ling Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| |
Collapse
|
18
|
Li Z, Li K, Yang X, Hao H, Jing HC. Combined QTL mapping and association study reveals candidate genes for leaf number and flowering time in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3459-3472. [PMID: 34247253 DOI: 10.1007/s00122-021-03907-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Twelve QTL for flowering and leaf number were detected. The ZmWRKY14Hap4 could increase leaf number, flowering time and biomass yield which are promising for silage maize breeding. Silage maize, one of the most important feedstock for ruminants, is widely grown from temperate regions to the tropics. Flowering time and leaf number are two significantly correlated traits and important for the quality, adaptation and biomass yield of silage maize. In this study, a recombinant inbred line population consisting of 215 individuals and an association panel of 369 inbred lines were analysed in field conditions in three locations for 2 consecutive years, and five, four and three quantitative trait loci for the total leaf number, days to anthesis (DTA) and silking (DTS) were detected, which could explain 48.55, 35.37 and 34.22% of total phenotypic variation, respectively. Association analysis of qLN10 on chromosome 10 found that ZmWRKY14 was the candidate gene for leaf number, whose expression level was negatively correlated with the leaf number. There are five haplotypes for ZmWRKY14, and haplotype 4 could significantly increase flowering time, leaf number and biomass yield, but has no obvious influence on ear weight. The optimal allelic combination of ZmWRKY14 and ZCN8 could further increase leaf number and biomass yield. The results will provide important genetic information for silage maize breeding.
Collapse
Affiliation(s)
- Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kun Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaohong Yang
- Beijing Key Laboratory of Crop Genetic Improvement, National Maize Improvement Centre of China, China Agricultural University, Beijing, 100193, China
| | - Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, China
- Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
19
|
Strable J. Developmental genetics of maize vegetative shoot architecture. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:19. [PMID: 37309417 PMCID: PMC10236122 DOI: 10.1007/s11032-021-01208-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/25/2021] [Indexed: 06/13/2023]
Abstract
More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01208-1.
Collapse
Affiliation(s)
- Josh Strable
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Present Address: Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 USA
| |
Collapse
|
20
|
Sun H, Wang C, Chen X, Liu H, Huang Y, Li S, Dong Z, Zhao X, Tian F, Jin W. dlf1 promotes floral transition by directly activating ZmMADS4 and ZmMADS67 in the maize shoot apex. THE NEW PHYTOLOGIST 2020; 228:1386-1400. [PMID: 32579713 DOI: 10.1111/nph.16772] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
The floral transition of the maize (Zea mays ssp. mays) shoot apical meristem determines leaf number and flowering time, which are key traits influencing local adaptation and yield potential. dlf1 (delayed flowering1) encodes a basic leucine zipper protein that interacts with the florigen ZCN8 to mediate floral induction in the shoot apex. However, the mechanism of how dlf1 promotes floral transition remains largely unknown. We demonstrate that dlf1 underlies qLB7-1, a quantitative trait locus controlling leaf number and flowering time that was identified in a BC2 S3 population derived from a cross between maize and its wild ancestor, teosinte (Zea mays ssp. parviglumis). Transcriptome sequencing and chromatin immunoprecipitation sequencing demonstrated that DLF1 binds the core promoter of two AP1/FUL subfamily MADS-box genes, ZmMADS4 and ZmMADS67, to activate their expression. Knocking out ZmMADS4 and ZmMADS67 both increased leaf number and delayed flowering, indicating that they promote the floral transition. Nucleotide diversity analysis revealed that dlf1 and ZmMADS67 were targeted by selection, suggesting that they may have played important roles in maize flowering time adaptation. We show that dlf1 promotes maize floral transition by directly activating ZmMADS4 and ZmMADS67 in the shoot apex, providing novel insights into the mechanism of maize floral transition.
Collapse
Affiliation(s)
- Huayue Sun
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Chenglong Wang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoyang Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Hongbing Liu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Yumin Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Suxing Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Zhao
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
21
|
Maize adaptation across temperate climates was obtained via expression of two florigen genes. PLoS Genet 2020; 16:e1008882. [PMID: 32673315 DOI: 10.1371/journal.pgen.1008882] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 07/28/2020] [Accepted: 05/22/2020] [Indexed: 11/19/2022] Open
Abstract
Expansion of the maize growing area was central for food security in temperate regions. In addition to the suppression of the short-day requirement for floral induction, it required breeding for a large range of flowering time that compensates the effect of South-North gradients of temperatures. Here we show the role of a novel florigen gene, ZCN12, in the latter adaptation in cooperation with ZCN8. Strong eQTLs of ZCN8 and ZCN12, measured in 327 maize lines, accounted for most of the genetic variance of flowering time in platform and field experiments. ZCN12 had a strong effect on flowering time of transgenic Arabidopsis thaliana plants; a path analysis showed that it directly affected maize flowering time together with ZCN8. The allelic composition at ZCN QTLs showed clear signs of selection by breeders. This suggests that florigens played a central role in ensuring a large range of flowering time, necessary for adaptation to temperate areas.
Collapse
|
22
|
Li H, Wang L, Liu M, Dong Z, Li Q, Fei S, Xiang H, Liu B, Jin W. Maize Plant Architecture Is Regulated by the Ethylene Biosynthetic Gene ZmACS7. PLANT PHYSIOLOGY 2020; 183:1184-1199. [PMID: 32321843 PMCID: PMC7333711 DOI: 10.1104/pp.19.01421] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/03/2020] [Indexed: 05/06/2023]
Abstract
Plant height and leaf angle are two crucial determinants of plant architecture in maize (Zea mays) and are closely related to lodging resistance and canopy photosynthesis at high planting density. These two traits are primarily regulated by several phytohormones. However, the mechanism of ethylene in regulating plant architecture in maize, especially plant height and leaf angle, is unclear. Here, we characterized a maize mutant, Semidwarf3 (Sdw3), which exhibits shorter stature and larger leaf angle than the wild type. Histological analysis showed that inhibition of longitudinal cell elongation in the internode and promotion in the auricle were mainly responsible for reduced plant height and enlarged leaf angle in the Sdw3 mutant. Through positional cloning, we identified a transposon insertion in the candidate gene ZmACS7, encoding 1-aminocyclopropane-1-carboxylic acid (ACC) Synthase 7 in ethylene biosynthesis of maize. The transposon alters the C terminus of ZmACS7. Transgenic analysis confirmed that the mutant ZmACS7 gene confers the phenotypes of the Sdw3 mutant. Enzyme activity and protein degradation assays indicated that the altered C terminus of ZmACS7 in the Sdw3 mutant increases this protein's stability but does not affect its catalytic activity. The ACC and ethylene contents are dramatically elevated in the Sdw3 mutant, leading to reduced plant height and increased leaf angle. In addition, we demonstrated that ZmACS7 plays crucial roles in root development, flowering time, and leaf number, indicating that ZmACS7 is an important gene with pleiotropic effects during maize growth and development.
Collapse
Affiliation(s)
- Hongchao Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, China
| | - Lijing Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Meishan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, China
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, China
| | - Qifang Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shulang Fei
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, China
| | - Hongtu Xiang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, China
| | - Baoshen Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, China
| |
Collapse
|
23
|
Chen Q, Samayoa LF, Yang CJ, Bradbury PJ, Olukolu BA, Neumeyer MA, Romay MC, Sun Q, Lorant A, Buckler ES, Ross-Ibarra J, Holland JB, Doebley JF. The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication. PLoS Genet 2020; 16:e1008791. [PMID: 32407310 PMCID: PMC7266358 DOI: 10.1371/journal.pgen.1008791] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/02/2020] [Accepted: 04/22/2020] [Indexed: 11/19/2022] Open
Abstract
The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is "missing" in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect.
Collapse
Affiliation(s)
- Qiuyue Chen
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Luis Fernando Samayoa
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chin Jian Yang
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Peter J. Bradbury
- US Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
| | - Bode A. Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Michael A. Neumeyer
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Maria Cinta Romay
- Genomic Diversity Facility, Cornell University, Ithaca, New York, United States of America
| | - Qi Sun
- Genomic Diversity Facility, Cornell University, Ithaca, New York, United States of America
| | - Anne Lorant
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Edward S. Buckler
- US Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - James B. Holland
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
- US Department of Agriculture–Agricultural Research Service Plant Science Research Unit, North Carolina State University, Raleigh, North Carolina, United States of America
| | - John F. Doebley
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
24
|
Dumas E, Feurtey A, Rodríguez de la Vega RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A, Giraud T. Independent domestication events in the blue-cheese fungus Penicillium roqueforti. Mol Ecol 2020; 29:2639-2660. [PMID: 31960565 PMCID: PMC7497015 DOI: 10.1111/mec.15359] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/02/2020] [Accepted: 01/04/2020] [Indexed: 12/13/2022]
Abstract
Domestication provides an excellent framework for studying adaptive divergence. Using population genomics and phenotypic assays, we reconstructed the domestication history of the blue cheese mould Penicillium roqueforti. We showed that this fungus was domesticated twice independently. The population used in Roquefort originated from an old domestication event associated with weak bottlenecks and exhibited traits beneficial for pre‐industrial cheese production (slower growth in cheese and greater spore production on bread, the traditional multiplication medium). The other cheese population originated more recently from the selection of a single clonal lineage, was associated with all types of blue cheese worldwide except Roquefort, and displayed phenotypes more suited for industrial cheese production (high lipolytic activity, efficient cheese cavity colonization ability and salt tolerance). We detected genomic regions affected by recent positive selection and putative horizontal gene transfers. This study sheds light on the processes of rapid adaptation and raises questions about genetic resource conservation. see also the Perspective by Brigida Gallone, Jan Steensels and Kevin J. Verstrepen.
Collapse
Affiliation(s)
- Emilie Dumas
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France.,Laboratory for Molecular Immunology and Inflammation, Department of Rheumatology, University Hospital Ghent, The Vlaams Instituut voor Biotechnologie (VIB) Center for Inflammation Research (IRC), Ghent, Belgium
| | - Alice Feurtey
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France.,Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Stéphanie Le Prieur
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Anne Thierry
- Science et Technologie du Lait et de l'Œuf (STLO), UMR1253, Agrocampus Ouest, INRAE, Rennes, France
| | - Emmanuel Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production - SAS L.I.P, Aurillac, France
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production - SAS L.I.P, Aurillac, France
| | - Jeanne Ropars
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Antoine Branca
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| |
Collapse
|
25
|
Das S, Parida SK, Agarwal P, Tyagi AK. Transcription factor OsNF-YB9 regulates reproductive growth and development in rice. PLANTA 2019; 250:1849-1865. [PMID: 31482329 DOI: 10.1007/s00425-019-03268-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 08/26/2019] [Indexed: 05/02/2023]
Abstract
OsNF-YB9 controls heading by affecting expression of regulators of flowering. It affects the development of the reproductive meristem by interacting with MADS1 and controlling expression of hormone-related genes. Nuclear Factor-Y (NF-Y) family of transcription factors takes part in many aspects of growth and development in eukaryotes. They have been classified into three subunit classes, namely, NF-YA, NF-YB and NF-YC. In plants, this transcription factor family is much diverged and takes part in several developmental processes and stress. We investigated NF-Y subunit genes of rice (Oryza sativa) and found OsNF-YB9 as the closest homologue of LEAFY COTYLEDON1. OsNF-YB9 delayed the heading date when ectopically expressed in rice. Expression of several heading date regulating genes such as Hd1, Ehd1, Hd3a and RFT1 were altered. OsNF-YB9 overexpression also resulted in morphological defects in the reproductive organs and led to pseudovivipary. OsNF-YB9 interacted with MADS1, a key regulator of floral development. This NF-Y subunit acted upstream to several transcription factors as well as signalling proteins involved in brassinosteroid and gibberellic acid metabolism and cell cycle. OsNF-YB9 and OsNF-YC12 interacted in planta and the latter also delayed heading in rice upon overexpression suggesting its involvement in a similar pathway. Our data provide new insights into the rice heading date pathway integrating these OsNF-Y subunit members to the network. These features can be exploited to improve vegetative growth and yield of rice plants in future.
Collapse
Affiliation(s)
- Sweta Das
- National Institute of Plant Genome Research, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, 110067, India.
| | - Akhilesh Kumar Tyagi
- National Institute of Plant Genome Research, New Delhi, 110067, India.
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.
| |
Collapse
|
26
|
Fustier MA, Martínez-Ainsworth NE, Aguirre-Liguori JA, Venon A, Corti H, Rousselet A, Dumas F, Dittberner H, Camarena MG, Grimanelli D, Ovaskainen O, Falque M, Moreau L, de Meaux J, Montes-Hernández S, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude. PLoS Genet 2019; 15:e1008512. [PMID: 31860672 PMCID: PMC6944379 DOI: 10.1371/journal.pgen.1008512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 01/06/2020] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation along the elevation gradient indicated that adaptation to altitude results from the assembly of multiple co-adapted traits into a complex syndrome: as elevation increases, plants flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele frequencies shifted along elevation as well as phenotypically-associated SNPs. Altogether, our results are consistent with the establishment of an altitudinal syndrome promoted by local selective forces in teosinte populations in spite of detectable gene flow. Because elevation mimics climate change through space, SNPs that we found underlying phenotypic variation at adaptive traits may be relevant for future maize breeding.
Collapse
Affiliation(s)
- Margaux-Alison Fustier
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Natalia E. Martínez-Ainsworth
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Jonás A. Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Anthony Venon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hélène Corti
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Agnès Rousselet
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Fabrice Dumas
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hannes Dittberner
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - María G. Camarena
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Daniel Grimanelli
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthieu Falque
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Laurence Moreau
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Juliette de Meaux
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yves Vigouroux
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Domenica Manicacci
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Maud I. Tenaillon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| |
Collapse
|
27
|
Li C, Wu X, Li Y, Shi Y, Song Y, Zhang D, Li Y, Wang T. Genetic architecture of phenotypic means and plasticities of kernel size and weight in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3309-3320. [PMID: 31555889 DOI: 10.1007/s00122-019-03426-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/11/2019] [Indexed: 05/11/2023]
Abstract
Genetic relationships between the phenotypic means and plasticities of kernel size and weight revealed the common genetic control of these traits in maize. Kernel size and weight are crucial components of grain yield in maize, and phenotypic plasticity in these traits facilitates adaptations to changing environments. Elucidating the genetic architecture of the mean phenotypic values and plasticities of kernel size and weight may be essential for breeding climate-robust maize varieties. Here, a maize nested association mapping (CN-NAM) population and association panel were grown in different environments. A joint linkage analysis and genome-wide association mapping were performed for five kernel size and weight phenotypic traits and two phenotypic plasticity measures. The mean phenotypes and plasticities were significantly correlated. The overall results of quantitative trait locus (QTL) and candidate gene analyses indicated moderate and high levels of common genetic control for the two traits. Furthermore, the mean phenotypes or plasticities of the hundred-kernel weight and volume were commonly regulated to a high degree. One pleiotropic locus on chromosome 10 simultaneously controlled the mean phenotypic values and plasticities of kernel size and weight. Therefore, the plasticity of kernel size and weight might be indirectly selected during maize breeding; however, selecting for high or low plasticity in combination with high or low mean phenotypic values of kernel size and weight traits may be difficult.
Collapse
Affiliation(s)
- Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xun Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| |
Collapse
|
28
|
Chen Q, Yang CJ, York AM, Xue W, Daskalska LL, DeValk CA, Krueger KW, Lawton SB, Spiegelberg BG, Schnell JM, Neumeyer MA, Perry JS, Peterson AC, Kim B, Bergstrom L, Yang L, Barber IC, Tian F, Doebley JF. TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize. Genetics 2019; 213:1065-1078. [PMID: 31481533 PMCID: PMC6827374 DOI: 10.1534/genetics.119.302594] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 08/30/2019] [Indexed: 12/21/2022] Open
Abstract
Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping (TeoNAM) population, derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and a genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTL from JLM were identified, with many of these mapping near known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTL for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.
Collapse
Affiliation(s)
- Qiuyue Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chin Jian Yang
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Alessandra M York
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Wei Xue
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Lora L Daskalska
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Craig A DeValk
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Kyle W Krueger
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Samuel B Lawton
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | | | - Jack M Schnell
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Michael A Neumeyer
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Joseph S Perry
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Aria C Peterson
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Brandon Kim
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Laura Bergstrom
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Liyan Yang
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
- School of Life Science, Shanxi Normal University, Linfen, Shanxi 041004, China
| | - Isaac C Barber
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Feng Tian
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - John F Doebley
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| |
Collapse
|
29
|
Xu G, Cao J, Wang X, Chen Q, Jin W, Li Z, Tian F. Evolutionary Metabolomics Identifies Substantial Metabolic Divergence between Maize and Its Wild Ancestor, Teosinte. THE PLANT CELL 2019; 31:1990-2009. [PMID: 31227559 PMCID: PMC6751114 DOI: 10.1105/tpc.19.00111] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/03/2019] [Accepted: 06/17/2019] [Indexed: 05/04/2023]
Abstract
Maize (Zea mays subsp mays) was domesticated from its wild ancestor, teosinte (Zea mays subsp parviglumis). Maize's distinct morphology and adaptation to diverse environments required coordinated changes in various metabolic pathways. However, how the metabolome was reshaped since domestication remains poorly understood. Here, we report a comprehensive assessment of divergence in the seedling metabolome between maize and teosinte. In total, 461 metabolites exhibited significant divergence due to selection. Interestingly, teosinte and tropical and temperate maize, representing major stages of maize evolution, targeted distinct sets of metabolites. Alkaloids, terpenoids, and lipids were specifically targeted in the divergence between teosinte and tropical maize, while benzoxazinoids were specifically targeted in the divergence between tropical and temperate maize. To identify genetic factors controlling metabolic divergence, we assayed the seedling metabolome of a large maize-by-teosinte cross population. We show that the recent metabolic divergence between tropical and temperate maize tended to have simpler genetic architecture than the divergence between teosinte and tropical maize. Through integrating transcriptome data, we identified candidate genes contributing to metabolic divergence, many of which were under selection at the nucleotide and transcript levels. Through overexpression or mutant analysis, we verified the roles of Flavanone 3-hydroxylase1, Purple aleurone1, and maize terpene synthase1 in the divergence of their related biosynthesis pathways. Our findings not only provide important insights into domestication-associated changes in the metabolism but also highlight the power of combining omics data for trait dissection.
Collapse
Affiliation(s)
- Guanghui Xu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jingjing Cao
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xufeng Wang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Qiuyue Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| |
Collapse
|
30
|
Dodig D, Božinović S, Nikolić A, Zorić M, Vančetović J, Ignjatović-Micić D, Delić N, Weigelt-Fischer K, Junker A, Altmann T. Image-Derived Traits Related to Mid-Season Growth Performance of Maize Under Nitrogen and Water Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:814. [PMID: 31297124 PMCID: PMC6607059 DOI: 10.3389/fpls.2019.00814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
Phenotypic measurements under controlled cultivation conditions are essential to gain a mechanistic understanding of plant responses to environmental impacts and thus for knowledge-based improvement of their performance under natural field conditions. Twenty maize inbred lines (ILs) were phenotyped in response to two levels of water and nitrogen supply (control and stress) and combined nitrogen and water deficit. Over a course of 5 weeks (from about 4-leaf stage to the beginning of the reproductive stage), maize phenology and growth were monitored by using a high-throughput phenotyping platform for daily acquisition of images in different spectral ranges. The focus of the present study is on the measurements taken at the time of maximum water stress (for traits that reflect plant physiological properties) and at the end of the experiment (for traits that reflect plant architectural and biomass-related traits). Twenty-five phenotypic traits extracted from the digital image data that support biological interpretation of plant growth were selected for their predictive value for mid-season shoot biomass accumulation. Measured fresh and dry weights after harvest were used to calculate various indices (water-use efficiency, physiological nitrogen-use efficiency, specific plant weight) and to establish correlations with image-derived phenotypic features. Also, score indices based on dry weight were used to identify contrasting ILs in terms of productivity and tolerance to stress, and their means for image-derived and manually measured traits were compared. Color-related traits appear to be indicative of plant performance and photosystem II operating efficiency might be an importance physiological parameter of biomass accumulation, particularly under severe stress conditions. Also, genotypes showing greater leaf area may be better adapted to abiotic stress conditions.
Collapse
Affiliation(s)
- Dejan Dodig
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Sofija Božinović
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Ana Nikolić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Miroslav Zorić
- Department for Maize, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Jelena Vančetović
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | | | - Nenad Delić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Kathleen Weigelt-Fischer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| |
Collapse
|
31
|
Blancon J, Dutartre D, Tixier MH, Weiss M, Comar A, Praud S, Baret F. A High-Throughput Model-Assisted Method for Phenotyping Maize Green Leaf Area Index Dynamics Using Unmanned Aerial Vehicle Imagery. FRONTIERS IN PLANT SCIENCE 2019; 10:685. [PMID: 31231403 PMCID: PMC6568052 DOI: 10.3389/fpls.2019.00685] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/07/2019] [Indexed: 05/19/2023]
Abstract
The dynamics of the Green Leaf Area Index (GLAI) is of great interest for numerous applications such as yield prediction and plant breeding. We present a high-throughput model-assisted method for characterizing GLAI dynamics in maize (Zea mays subsp. mays) using multispectral imagery acquired from an Unmanned Aerial Vehicle (UAV). Two trials were conducted with a high diversity panel of 400 lines under well-watered and water-deficient treatments in 2016 and 2017. For each UAV flight, we first derived GLAI estimates from empirical relationships between the multispectral reflectance and ground level measurements of GLAI achieved over a small sample of microplots. We then fitted a simple but physiologically sound GLAI dynamics model over the GLAI values estimated previously. Results show that GLAI dynamics was estimated accurately throughout the cycle (R2 > 0.9). Two parameters of the model, biggest leaf area and leaf longevity, were also estimated successfully. We showed that GLAI dynamics and the parameters of the fitted model are highly heritable (0.65 ≤ H2 ≤ 0.98), responsive to environmental conditions, and linked to yield and drought tolerance. This method, combining growth modeling, UAV imagery and simple non-destructive field measurements, provides new high-throughput tools for understanding the adaptation of GLAI dynamics and its interaction with the environment. GLAI dynamics is also a promising trait for crop breeding, and paves the way for future genetic studies.
Collapse
Affiliation(s)
- Justin Blancon
- Biogemma, Centre de Recherche de Chappes, Chappes, France
| | | | | | - Marie Weiss
- INRA UMR 114 EMMAH, UMT CAPTE, Domaine Saint-Paul, Avignon, France
| | | | | | - Frédéric Baret
- INRA UMR 114 EMMAH, UMT CAPTE, Domaine Saint-Paul, Avignon, France
| |
Collapse
|
32
|
Cao Y, Liang X, Yin P, Zhang M, Jiang C. A domestication-associated reduction in K + -preferring HKT transporter activity underlies maize shoot K + accumulation and salt tolerance. THE NEW PHYTOLOGIST 2019; 222:301-317. [PMID: 30461018 DOI: 10.1111/nph.15605] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/10/2018] [Indexed: 05/26/2023]
Abstract
Maize was domesticated from Balsas teosinte c. 10 000 yr ago. Previous studies have suggested that increased tolerance to environmental stress occurred during maize domestication. However, the underlying genetic basis remains largely unknown. We used a maize (W22)-teosinte recombinant inbred line (RIL) to investigate the salt wild-type tolerance aspects of maize domestication. We revealed that ZmHKT2 is a major QTL that regulates K+ homeostasis in saline soils. ZmHKT2 encodes a K+ -preferring HKT family transporter and probably reduces shoot K+ content by removing K+ ions from root-to-shoot flowing xylem sap, ZmHKT2 deficiency increases xylem sap and shoot K+ concentrations, and increases salt tolerance. A coding sequence polymorphism in the ZmHKT2W22 allele (SNP389-G) confers an amino acid variant ZmHKT2 that increases xylem sap K+ concentration, thereby increasing shoot K+ content and salt tolerance. Additional analyses showed that SNP389-G first existed in teosinte (allele frequency 56% in assayed accessions), then swept through the maize population (allele frequency 98%), and that SNP389-G probably underwent positive selection during maize domestication. We conclude that a domestication-associated reduction in K+ transport activity in ZmHKT2 underlies maize shoot K+ content and salt tolerance, and propose that CRISPR-based editing of ZmHKT2 might provide a feasible strategy for improving maize salt tolerance.
Collapse
Affiliation(s)
- Yibo Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Xiaoyan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Pan Yin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Ming Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Caifu Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| |
Collapse
|
33
|
Liang Y, Liu Q, Wang X, Huang C, Xu G, Hey S, Lin HY, Li C, Xu D, Wu L, Wang C, Wu W, Xia J, Han X, Lu S, Lai J, Song W, Schnable PS, Tian F. ZmMADS69 functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to maize flowering time adaptation. THE NEW PHYTOLOGIST 2019; 221:2335-2347. [PMID: 30288760 DOI: 10.1111/nph.15512] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/14/2018] [Indexed: 05/26/2023]
Abstract
Flowering time is a major determinant of the local adaptation of plants. Although numerous loci affecting flowering time have been mapped in maize, their underlying molecular mechanisms and roles in adaptation remain largely unknown. Here, we report the identification and characterization of MADS-box transcription factor ZmMADS69 that functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to adaptation. We show that ZmMADS69 underlies a quantitative trait locus controlling the difference in flowering time between maize and its wild ancestor, teosinte. Maize ZmMADS69 allele is expressed at a higher level at floral transition and confers earlier flowering than the teosinte allele under long days and short days. Overexpression of ZmMADS69 causes early flowering, while a transposon insertion mutant of ZmMADS69 exhibits delayed flowering. ZmMADS69 shows pleiotropic effects for multiple traits of agronomic importance. ZmMADS69 functions upstream of the flowering repressor ZmRap2.7 to downregulate its expression, thereby relieving the repression of the florigen gene ZCN8 and causing early flowering. Population genetic analyses showed that ZmMADS69 was a target of selection and may have played an important role as maize spread from the tropics to temperate zones. Our findings provide important insights into the regulation and adaptation of flowering time.
Collapse
Affiliation(s)
- Yameng Liang
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qiang Liu
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
| | - Xufeng Wang
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Cheng Huang
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Guanghui Xu
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Stefan Hey
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
| | - Hung-Ying Lin
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
| | - Cong Li
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Dingyi Xu
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lishuan Wu
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chenglong Wang
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weihao Wu
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinliang Xia
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xu Han
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Sijia Lu
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jinsheng Lai
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weibin Song
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
- Department of Plant Genetics & Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Tian
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
34
|
Cui Z, Xia A, Zhang A, Luo J, Yang X, Zhang L, Ruan Y, He Y. Linkage mapping combined with association analysis reveals QTL and candidate genes for three husk traits in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2131-2144. [PMID: 30043259 DOI: 10.1007/s00122-018-3142-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
Key message Combined linkage and association mapping analyses facilitate the emphasis on the candidate genes putatively involved in maize husk growth. The maize (Zea mays L.) husk consists of multiple leafy layers and plays important roles in protecting the ear from pathogen infection and in preventing grain dehydration. Although husk morphology varies widely among different maize inbred lines, the genetic basis of such variation is poorly understood. In this study, we used three maize recombinant inbred line (RIL) populations to dissect the genetic basis of three husk traits: i.e., husk length (HL), husk width (HW), and the number of husk layers (HN). Three husk traits in all three RIL populations showed wide phenotypic variation and high heritability. The HL showed stronger correlations with ear traits than did HW and HN. A total of 21 quantitative trait loci (QTL) were identified for the three traits in three RIL populations, and some of them were commonly observed for the same trait in different populations. The proportions of total phenotypic variation explained by QTL in three RIL populations were 31.8, 35.3, and 44.5% for HL, HW, and HN, respectively. The highest proportions of phenotypic variation explained by a single QTL were 14.7% for HL in the By815/K22 RIL population (BYK), 13.5% for HW in the By815/DE3 RIL population (BYD), and 19.4% for HN in the BYD population. A combined analysis of linkage mapping with a previous genome-wide association study revealed five candidate genes related to husk morphology situated within three QTL loci. These five genes were related to metabolism, gene expression regulation, and signal transduction.
Collapse
Affiliation(s)
- Zhenhai Cui
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Aiai Xia
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Ao Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jinhong Luo
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Lijun Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yanye Ruan
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.
| |
Collapse
|
35
|
Maize yields over Europe may increase in spite of climate change, with an appropriate use of the genetic variability of flowering time. Proc Natl Acad Sci U S A 2018; 115:10642-10647. [PMID: 30275304 PMCID: PMC6196545 DOI: 10.1073/pnas.1720716115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The consequences of climate change on European maize yields may become positive if farmers in 2050 use the decision rules they currently follow for adapting plant cycle duration and sowing dates to the diversity of environmental conditions. Experiments and simulations show that the current genetic variability of flowering time allows identifying a cycle duration that maximizes yield at every maize field in Europe. The assumption that farmers use this optimal cycle length in each site was supported by comparison with historical data. Simulated European production for 2050 was stable under the hypotheses of unchanged practices but was increased if farmers continued adopting the decision rules they currently use for adjusting sowing date and crop cycle duration to local environment. Projections based on invariant genotypes and agronomic practices indicate that climate change will largely decrease crop yields. The comparatively few studies considering farmers’ adaptation result in a diversity of impacts depending on their assumptions. We combined experiments and process-based modeling for analyzing the consequences of climate change on European maize yields if farmers made the best use of the current genetic variability of cycle duration, based on practices they currently use. We first showed that the genetic variability of maize flowering time is sufficient for identifying a cycle duration that maximizes yield in a range of European climatic conditions. This was observed in six field experiments with a panel of 121 accessions and extended to 59 European sites over 36 years with a crop model. The assumption that farmers use optimal cycle duration and sowing date was supported by comparison with historical data. Simulations were then carried out for 2050 with 3 million combinations of crop cycle durations, climate scenarios, management practices, and modeling hypotheses. Simulated grain production over Europe in 2050 was stable (−1 to +1%) compared with the 1975–2010 baseline period under the hypotheses of unchanged cycle duration, whereas it was increased (+4–7%) when crop cycle duration and sowing dates were optimized in each local environment. The combined effects of climate change and farmer adaptation reduced the yield gradient between south and north of Europe and increased European maize production if farmers continued to make the best use of the genetic variability of crop cycle duration.
Collapse
|
36
|
Guo L, Wang X, Zhao M, Huang C, Li C, Li D, Yang CJ, York AM, Xue W, Xu G, Liang Y, Chen Q, Doebley JF, Tian F. Stepwise cis-Regulatory Changes in ZCN8 Contribute to Maize Flowering-Time Adaptation. Curr Biol 2018; 28:3005-3015.e4. [PMID: 30220503 DOI: 10.1016/j.cub.2018.07.029] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/24/2018] [Accepted: 07/09/2018] [Indexed: 12/28/2022]
Abstract
Maize (Zea mays ssp. mays) was domesticated in southwestern Mexico ∼9,000 years ago from its wild ancestor, teosinte (Zea mays ssp. parviglumis) [1]. From its center of origin, maize experienced a rapid range expansion and spread over 90° of latitude in the Americas [2-4], which required a novel flowering-time adaptation. ZEA CENTRORADIALIS 8 (ZCN8) is the maize florigen gene and has a central role in mediating flowering [5, 6]. Here, we show that ZCN8 underlies a major quantitative trait locus (QTL) (qDTA8) for flowering time that was consistently detected in multiple maize-teosinte experimental populations. Through association analysis in a large diverse panel of maize inbred lines, we identified a SNP (SNP-1245) in the ZCN8 promoter that showed the strongest association with flowering time. SNP-1245 co-segregated with qDTA8 in maize-teosinte mapping populations. We demonstrate that SNP-1245 is associated with differential binding by the flowering activator ZmMADS1. SNP-1245 was a target of selection during early domestication, which drove the pre-existing early flowering allele to near fixation in maize. Interestingly, we detected an independent association block upstream of SNP-1245, wherein the early flowering allele that most likely originated from Zea mays ssp. mexicana introgressed into the early flowering haplotype of SNP-1245 and contributed to maize adaptation to northern high latitudes. Our study demonstrates how independent cis-regulatory variants at a gene can be selected at different evolutionary times for local adaptation, highlighting how complex cis-regulatory control mechanisms evolve. Finally, we propose a polygenic map for the pre-Columbian spread of maize throughout the Americas.
Collapse
Affiliation(s)
- Li Guo
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xuehan Wang
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Min Zhao
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Cheng Huang
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Cong Li
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Dan Li
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chin Jian Yang
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Alessandra M York
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Wei Xue
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Guanghui Xu
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yameng Liang
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Qiuyue Chen
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China; Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Feng Tian
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
37
|
Jiménez-Galindo JC, Malvar RA, Butrón A, Caicedo M, Ordás B. Fine analysis of a genomic region involved in resistance to Mediterranean corn borer. BMC PLANT BIOLOGY 2018; 18:169. [PMID: 30111285 PMCID: PMC6094900 DOI: 10.1186/s12870-018-1385-3] [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: 11/15/2017] [Accepted: 08/01/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Sesamia nonagrioides Lefebvere (Mediterranean corn borer, MCB) is the main pest of maize in the Mediterranean area. QTL for MCB stalk tunneling and grain yield under high MCB infestation had been located at bin 8.03-8.05 (4-21 cM and 10-30 cM respectively) in a previous analysis of the EP42 x EP39 RILs mapping population. The objective of the present work was to study with higher resolution those QTL, and validating and estimating with higher precision their locations and effects. To achieve this objective, we developed a set of 38 heterogeneous inbred families (HIFs) which were near-homozygous in the genome, except in the region under study. The HIFs were evaluated in multiple environments under artificial infestation with MCB and genotyped with SNPs. RESULTS The QTL for grain yield under high infestation was confirmed with higher precision and improved reliability at 112.6-116.9 Mb. On the contrary, the location of the QTL for stalk tunneling was not validated probably due to the fixation of some genomic regions during the development of the HIFs. Our study confirmed that the co-localization of the QTL for stalk tunneling and grain yield in the previous study was due to linked genes, not to pleiotropic effects. So, the QTL for grain yield can be used for improving grain yield without undesirable effect on stalk tunneling. CONCLUSIONS The HIF analysis is useful for validating QTL and for conducting deeper studies in traits related to corn borer resistance.
Collapse
Affiliation(s)
- José Cruz Jiménez-Galindo
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
- National Institute of Forestry, Agriculture and Livestock Research (INIFAP), Ave. Hidalgo 1213, Cd., 31500 Cuauhtémoc, Chihuahua, Mexico
| | - Rosa Ana Malvar
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| | - Ana Butrón
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| | - Marlon Caicedo
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
- National Institute of Agricultural Research (INIAP), 170315 Quito, Ecuador
| | - Bernardo Ordás
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080 Pontevedra, Spain
| |
Collapse
|
38
|
Huang C, Sun H, Xu D, Chen Q, Liang Y, Wang X, Xu G, Tian J, Wang C, Li D, Wu L, Yang X, Jin W, Doebley JF, Tian F. ZmCCT9 enhances maize adaptation to higher latitudes. Proc Natl Acad Sci U S A 2018; 115:E334-E341. [PMID: 29279404 DOI: 10.1073/pnas.1718058115/suppl_file/pnas.1718058115.sapp.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
From its tropical origin in southwestern Mexico, maize spread over a wide latitudinal cline in the Americas. This feat defies the rule that crops are inhibited from spreading easily across latitudes. How the widespread latitudinal adaptation of maize was accomplished is largely unknown. Through positional cloning and association mapping, we resolved a flowering-time quantitative trait locus to a Harbinger-like transposable element positioned 57 kb upstream of a CCT transcription factor (ZmCCT9). The Harbinger-like element acts in cis to repress ZmCCT9 expression to promote flowering under long days. Knockout of ZmCCT9 by CRISPR/Cas9 causes early flowering under long days. ZmCCT9 is diurnally regulated and negatively regulates the expression of the florigen ZCN8, thereby resulting in late flowering under long days. Population genetics analyses revealed that the Harbinger-like transposon insertion at ZmCCT9 and the CACTA-like transposon insertion at another CCT paralog, ZmCCT10, arose sequentially following domestication and were targeted by selection for maize adaptation to higher latitudes. Our findings help explain how the dynamic maize genome with abundant transposon activity enabled maize to adapt over 90° of latitude during the pre-Columbian era.
Collapse
Affiliation(s)
- Cheng Huang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Huayue Sun
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Dingyi Xu
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Qiuyue Chen
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yameng Liang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xufeng Wang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Guanghui Xu
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jinge Tian
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chenglong Wang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Dan Li
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Lishuan Wu
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Weiwei Jin
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - John F Doebley
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Feng Tian
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China;
| |
Collapse
|
39
|
Abstract
Flowering time is a critical determinant of crop adaptation to local environments. As a result of natural and artificial selection, maize has evolved a reduced photoperiod sensitivity to adapt to regions over 90° of latitude in the Americas. Here we show that a distant Harbinger-like transposon acts as a cis-regulatory element to repress ZmCCT9 expression to promote flowering under the long days of higher latitudes. The transposon at ZmCCT9 and another functional transposon at a second flowering-time gene, ZmCCT10, arose sequentially following domestication and were targeted by selection as maize spread from the tropics to higher latitudes. Our results demonstrate that new functional variation created by transposon insertions helped maize to spread over a broad range of latitudes rapidly. From its tropical origin in southwestern Mexico, maize spread over a wide latitudinal cline in the Americas. This feat defies the rule that crops are inhibited from spreading easily across latitudes. How the widespread latitudinal adaptation of maize was accomplished is largely unknown. Through positional cloning and association mapping, we resolved a flowering-time quantitative trait locus to a Harbinger-like transposable element positioned 57 kb upstream of a CCT transcription factor (ZmCCT9). The Harbinger-like element acts in cis to repress ZmCCT9 expression to promote flowering under long days. Knockout of ZmCCT9 by CRISPR/Cas9 causes early flowering under long days. ZmCCT9 is diurnally regulated and negatively regulates the expression of the florigen ZCN8, thereby resulting in late flowering under long days. Population genetics analyses revealed that the Harbinger-like transposon insertion at ZmCCT9 and the CACTA-like transposon insertion at another CCT paralog, ZmCCT10, arose sequentially following domestication and were targeted by selection for maize adaptation to higher latitudes. Our findings help explain how the dynamic maize genome with abundant transposon activity enabled maize to adapt over 90° of latitude during the pre-Columbian era.
Collapse
|
40
|
Pan Q, Xu Y, Li K, Peng Y, Zhan W, Li W, Li L, Yan J. The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations. PLANT PHYSIOLOGY 2017; 175:858-873. [PMID: 28838954 PMCID: PMC5619899 DOI: 10.1104/pp.17.00709] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/21/2017] [Indexed: 05/02/2023]
Abstract
Plant architecture is a key factor affecting planting density and grain yield in maize (Zea mays). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3, has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding.
Collapse
Affiliation(s)
- Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuancheng Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
41
|
Cui M, Jia B, Liu H, Kan X, Zhang Y, Zhou R, Li Z, Yang L, Deng D, Yin Z. Genetic Mapping of the Leaf Number above the Primary Ear and Its Relationship with Plant Height and Flowering Time in Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:1437. [PMID: 28868062 PMCID: PMC5563357 DOI: 10.3389/fpls.2017.01437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/03/2017] [Indexed: 06/01/2023]
Abstract
The leaf number above the primary ear (LA) is a major contributing factor to plant architecture in maize. The yield of leafy maize, which has extra LA compared to normal maize, is higher than normal maize in some regions. One major concern is that increasing LA may be accompanied by increased plant height and/or flowering time. Using an F2:3 population comprising 192 families derived from a leafy maize line and a normal maize line, an association population comprising 437 inbred maize lines, and a pair of near-isogenic maize lines, we mapped the quantitative trait loci (QTL) associated with LA and assessed its genetic relationship with flowering time and plant height. Ten QTL with an additive and dominant effect, 18 pairs of interacting QTL in the F2:3 population and seventeen significant SNPs in the association population were detected for LA. Two major QTL, qLA3-4 and qLA7-1, were repeatedly detected and explained a large proportion of the phenotypic variation. The qLA3-4 was centered on lfy1, which is a dominant gene underlying extra leaves above the ear in leafy maize. Four LA QTL were found to overlap with flowering time and/or plant height, which suggested that these QTL might have a pleiotropic effect. The pleiotropy of the lfy1 locus on LA, flowering time and plant height were validated by near-isogenic line analysis. These results enhance our understanding of the genetic architecture affecting maize LA and the development of maize hybrids with increased LA.
Collapse
Affiliation(s)
- Min Cui
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Bo Jia
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in JiangsuHuai’an, China
| | - Huanhuan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Xin Kan
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Yu Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Ronghua Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Zhipeng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Liang Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Dexiang Deng
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| | - Zhitong Yin
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou UniversityYangzhou, China
| |
Collapse
|
42
|
Li H, Yang Q, Fan N, Zhang M, Zhai H, Ni Z, Zhang Y. Quantitative trait locus analysis of heterosis for plant height and ear height in an elite maize hybrid zhengdan 958 by design III. BMC Genet 2017; 18:36. [PMID: 28415964 PMCID: PMC5392948 DOI: 10.1186/s12863-017-0503-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/06/2017] [Indexed: 11/23/2022] Open
Abstract
Background Plant height (PH) and ear height (EH) are two important agronomic traits in maize selection breeding. F1 hybrid exhibit significant heterosis for PH and EH as compared to their parental inbred lines. To understand the genetic basis of heterosis controlling PH and EH, we conducted quantitative trait locus (QTL) analysis using a recombinant inbreed line (RIL) based design III population derived from the elite maize hybrid Zhengdan 958 in five environments. Results A total of 14 environmentally stable QTLs were identified, and the number of QTLs for Z1 and Z2 populations was six and eight, respectively. Notably, all the eight environmentally stable QTLs for Z2 were characterized by overdominance effect (OD), suggesting that overdominant QTLs were the most important contributors to heterosis for PH and EH. Furthermore, 14 environmentally stable QTLs were anchored on six genomic regions, among which four are trait-specific QTLs, suggesting that the genetic basis for PH and EH is partially different. Additionally, qPH.A-1.3, modifying about 10 centimeters of PH, was further validated in backcross populations. Conclusions The genetic basis for PH and EH is partially different, and overdominant QTLs are important factors for heterosis of PH and EH. A major QTL qPH.A-1.3 may be a desired target for genetic improvement of maize plant height. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0503-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hongjian Li
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Qingsong Yang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China.,National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Nannan Fan
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China.,National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Ming Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Huijie Zhai
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China
| | - Yirong Zhang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis Utilization (MOE), China Agricultural University, Beijing, 100193, China. .,National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
43
|
Xu G, Wang X, Huang C, Xu D, Li D, Tian J, Chen Q, Wang C, Liang Y, Wu Y, Yang X, Tian F. Complex genetic architecture underlies maize tassel domestication. THE NEW PHYTOLOGIST 2017; 214:852-864. [PMID: 28067953 PMCID: PMC5363343 DOI: 10.1111/nph.14400] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/16/2016] [Indexed: 05/02/2023]
Abstract
Maize (Zea mays) tassels underwent profound morphological changes during maize domestication and improvement. Although a number of genes affecting maize inflorescence development have been identified, the genetic basis of the morphological changes in maize tassels since domestication is not well understood. Here, using a large population of 866 maize-teosinte BC2 S3 recombinant inbred lines genotyped using 19 838 single nucleotide polymorphism (SNP) markers, we performed high-resolution quantitative trait locus (QTL) mapping for five tassel morphological traits. We showed that the five tassel traits were associated with different genetic architecture features. Known genes for maize inflorescence development identified by mutagenesis were significantly enriched in the tassel trait QTLs, and many of these genes, including ramosa1 (ra1), barren inflorescence2 (bif2), unbranched2 (ub2), zea floricaula leafy2 (zfl2) and barren stalk fastigiate1 (baf1), showed evidence of selection. An in-depth nucleotide diversity analysis at the bif2 locus identified strong selection signatures in the 5'-regulatory region. We also found that several known flowering time genes co-localized with tassel trait QTLs. A further association analysis indicated that the maize photoperiod gene ZmCCT was significantly associated with tassel size variation. Using near-isogenic lines, we narrowed down a major-effect QTL for tassel length, qTL9-1, to a 513-kb physical region. These results provide important insights into the genetic architecture that controls maize tassel evolution.
Collapse
Affiliation(s)
- Guanghui Xu
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Xufeng Wang
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Cheng Huang
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Dingyi Xu
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Dan Li
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Jinge Tian
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Qiuyue Chen
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Chenglong Wang
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Yameng Liang
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Yaoyao Wu
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Xiaohong Yang
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| | - Feng Tian
- National Maize Improvement CenterChina Agricultural UniversityBeijing100193China
| |
Collapse
|