1
|
Dzievit MJ, Li X, Yu J. Genetic mapping of dynamic control of leaf angle across multiple canopy levels in maize. THE PLANT GENOME 2024; 17:e20423. [PMID: 38123363 DOI: 10.1002/tpg2.20423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/22/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023]
Abstract
Optimizing leaf angle and other canopy architecture traits has helped modern maize (Zea mays L.) become adapted to higher planting densities over the last 60 years. Traditional investigations into genetic control of leaf angle have focused on one leaf or the average of multiple leaves; as a result, our understanding of genetic control across multiple canopy levels is still limited. To address this, genetic mapping across four canopy levels was conducted in the present study to investigate the genetic control of leaf angle across the canopy. We developed two populations of doubled haploid lines derived from three inbreds with distinct leaf angle phenotypes. These populations were genotyped with genotyping-by-sequencing and phenotyped for leaf angle at four different canopy levels over multiple years. To understand how leaf angle changes across the canopy, the four measurements were used to derive three additional traits. Composite interval mapping was conducted with the leaf-specific measurements and the derived traits. A set of 59 quantitative trait loci (QTLs) were uncovered for seven traits, and two genomic regions were consistently detected across multiple canopy levels. Additionally, seven genomic regions were found to contain consistent QTLs with either relatively stable or dynamic effects at different canopy levels. Prioritizing the selection of QTLs with dynamic effects across the canopy will aid breeders in selecting maize hybrids with the ideal canopy architecture that continues to maximize yield on a per area basis under increasing planting densities.
Collapse
Affiliation(s)
| | - Xianran Li
- USDA-ARS, Wheat Health, Genetics, and Quality Research, Pullman, Washington, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| |
Collapse
|
2
|
Li C, Li Y, Song G, Yang D, Xia Z, Sun C, Zhao Y, Hou M, Zhang M, Qi Z, Wang B, Wang H. Gene expression and expression quantitative trait loci analyses uncover natural variations underlying the improvement of important agronomic traits during modern maize breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:772-787. [PMID: 37186341 DOI: 10.1111/tpj.16260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/17/2023]
Abstract
Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant have contributed significantly to the increased yield per unit land area. Systematically identifying key agronomic traits and their associated genomic changes during modern maize breeding remains a significant challenge because of the complexity of genetic regulation and the interactions of the various agronomic traits, with most of them being controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 elite inbred lines of maize from different breeding eras in China. We found four yield-related traits are significantly improved during modern maize breeding. Through gene-clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene co-expression network analysis, we identified several candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining expression quantitative trait loci (eQTLs) analyses, correlation coefficient analyses and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2 and ZmPYL10 that influence kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for the molecular breeding of maize cultivars with tolerance for high-density planting.
Collapse
Affiliation(s)
- Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, 010070, China
| | - Yaoyao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Guangshu Song
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Di Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhanchao Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Changhe Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuelei Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingyue Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhi Qi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, 010070, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| |
Collapse
|
3
|
Zhu Y, Song B, Guo Y, Wang B, Xu C, Zhu H, E L, Lai J, Song W, Zhao H. QTL Analysis Reveals Conserved and Differential Genetic Regulation of Maize Lateral Angles above the Ear. PLANTS (BASEL, SWITZERLAND) 2023; 12:680. [PMID: 36771763 PMCID: PMC9920044 DOI: 10.3390/plants12030680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Improving the density tolerance and planting density has great importance for increasing maize production. The key to promoting high density planting is breeding maize with a compact canopy architecture, which is mainly influenced by the angles of the leaves and tassel branches above the ear. It is still unclear whether the leaf angles of different stem nodes and tassel branches are controlled by similar genetic regulatory mechanisms, which limits the ability to breed for density-tolerant maize. Here, we developed a population with 571 double haploid lines derived from inbred lines, PHBA6 and Chang7-2, showing significant differences in canopy architecture. Phenotypic and QTL analyses revealed that the genetic regulation mechanism was largely similar for closely adjacent leaves above the ears. In contrast, the regulation mechanisms specifying the angles of distant leaves and the angles of leaves vs. tassel branches are largely different. The liguless1 gene was identified as a candidate gene for QTLs co-regulating the angles of different leaves and the tassel branch, consistent with its known roles in regulating plant architecture. Our findings can be used to develop strategies for the improvement of leaf and tassel architecture through the introduction of trait-specific or pleiotropic genes, thus benefiting the breeding of maize with increased density tolerance in the future.
Collapse
Affiliation(s)
- Yanbin Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd., Shenyang 110164, China
- Sanya Institute of Henan University, Sanya 572025, China
| | - Bo Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd., Shenyang 110164, China
| | - Yanling Guo
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd., Shenyang 110164, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Changcheng Xu
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd., Shenyang 110164, China
| | - Hongyu Zhu
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd., Shenyang 110164, China
| | - Lizhu E
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Haiming Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| |
Collapse
|
4
|
Wu S, Wang J, Zhao Y, Wen W, Zhang Y, Lu X, Wang C, Liu K, Chen B, Guo X, Zhao C. Characterization and genetic dissection of maize ear leaf midrib acquired by 3D digital technology. FRONTIERS IN PLANT SCIENCE 2022; 13:1063056. [PMID: 36531364 PMCID: PMC9754214 DOI: 10.3389/fpls.2022.1063056] [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: 10/06/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
The spatial morphological structure of plant leaves is an important index to evaluate crop ideotype. In this study, we characterized the three-dimensional (3D) data of the ear leaf midrib of maize at the grain-filling stage using the 3D digitization technology and obtained the phenotypic values of 15 traits covering four different dimensions of the ear leaf midrib, of which 13 phenotypic traits were firstly proposed for featuring plant leaf spatial structure. Cluster analysis results showed that the 13 traits could be divided into four groups, Group I, -II, -III and -IV. Group I contains HorizontalLength, OutwardGrowthMeasure, LeafAngle and DeviationTip; Group II contains DeviationAngle, MaxCurvature and CurvaturePos; Group III contains LeafLength and ProjectionArea; Group IV contains TipTop, VerticalHeight, UpwardGrowthMeasure, and CurvatureRatio. To investigate the genetic basis of the ear leaf midrib curve, 13 traits with high repeatability were subjected to genome-wide association study (GWAS) analysis. A total of 828 significantly related SNPs were identified and 1365 candidate genes were annotated. Among these, 29 candidate genes with the highest significant and multi-method validation were regarded as the key findings. In addition, pathway enrichment analysis was performed on the candidate genes of traits to explore the potential genetic mechanism of leaf midrib curve phenotype formation. These results not only contribute to further understanding of maize leaf spatial structure traits but also provide new genetic loci for maize leaf spatial structure to improve the plant type of maize varieties.
Collapse
Affiliation(s)
- Sheng Wu
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Jinglu Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA (DeoxyriboNucleic Acid) Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Weiliang Wen
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Ying Zhang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Xianju Lu
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Chuanyu Wang
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Kai Liu
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Bo Chen
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Xinyu Guo
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Chunjiang Zhao
- Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| |
Collapse
|
5
|
Duan H, Li J, Sun Y, Xiong X, Sun L, Li W, Gao J, Li N, Zhang J, Cui J, Fu Z, Zhang X, Tang J. Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis. Front Genet 2022; 13:1004211. [PMID: 36437932 PMCID: PMC9691904 DOI: 10.3389/fgene.2022.1004211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022] Open
Abstract
Leaf angle (LA) is a key component of maize plant architecture that can simultaneously govern planting density and improve final yield. However, the genetic mechanisms underlying LA have not been fully addressed. To broaden our understanding of its genetic basis, we scored three LA-related traits on upper, middle, and low leaves of 492 maize inbred lines in five environments. Phenotypic data revealed that the three LA-related traits were normally distributed, and significant variation was observed among environments and genotypes. A genome-wide association study (GWAS) was then performed to dissect the genetic factors that control natural variation in maize LA. In total, 85 significant SNPs (involving 32 non-redundant QTLs) were detected (p ≤ 2.04 × 10–6), and individual QTL explained 4.80%–24.09% of the phenotypic variation. Five co-located QTL were detected in at least two environments, and two QTLs were co-located with multiple LA-related traits. Forty-seven meta-QTLs were identified based on meta-analysis combing 294 LA-related QTLs extracted from 18 previously published studies, 816 genes were identified within these meta-QTLs, and seven co-located QTLs were jointly identified by both GWAS and meta-analysis. ZmULA1 was located in one of the co-located QTLs, qLA7, and its haplotypes, hap1 and hap2, differed significantly in LA-related traits. Interestingly, the temperate materials with hap2 had smallest LA. Finally, we also performed haplotype analysis using the reported genes that regulate LA, and identified a lot of maize germplasms that aggregated favorable haplotypes. These results will be helpful for elucidating the genetic basis of LA and breeding new maize varieties with ideal plant architecture.
Collapse
Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Wenlong Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Na Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Junli Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiangkuan Cui
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Xuehai Zhang, ; Jihua Tang,
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
- *Correspondence: Xuehai Zhang, ; Jihua Tang,
| |
Collapse
|
6
|
Messina CD, Rotundo J, Hammer GL, Gho C, Reyes A, Fang Y, van Oosterom E, Borras L, Cooper M. Radiation use efficiency increased over a century of maize (Zea mays L.) breeding in the US corn belt. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5503-5513. [PMID: 35640591 DOI: 10.1093/jxb/erac212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/23/2022] [Indexed: 05/26/2023]
Abstract
In the absence of stress, crop growth depends on the amount of light intercepted by the canopy and the conversion efficiency [radiation use efficiency (RUE)]. This study tested the hypothesis that long-term genetic gain for grain yield was partly due to improved RUE. The hypothesis was tested using 30 elite maize hybrids commercialized in the US corn belt between 1930 and 2017. Crops grown under irrigation showed that pre-flowering crop growth increased at a rate of 0.11 g m-2 year-1, while light interception remained constant. Therefore, RUE increased at a rate of 0.0049 g MJ-1 year-1, translating into an average of 3 g m-2 year-1 of grain yield over 100 years of maize breeding. Considering that the harvest index has not changed for crops grown at optimal density for the hybrid, the cumulative RUE increase over the history of commercial maize breeding in the USA can account for ~32% of the documented yield trend for maize grown in the central US corn belt. The remaining RUE gap between this study and theoretical maximum values suggests that a yield improvement of a similar magnitude could be achieved by further increasing RUE.
Collapse
Affiliation(s)
- Carlos D Messina
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Jose Rotundo
- Corteva Agriscience, 8305 62nd Avenue, Johnston, IA 50131, USA
| | - Graeme L Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Carla Gho
- Corteva Agriscience, 8305 62nd Avenue, Johnston, IA 50131, USA
| | - Andres Reyes
- Corteva Agriscience, 18369 County Rd 96, Woodland, CA, USA
| | - Yinan Fang
- Corteva Agriscience, 8305 62nd Avenue, Johnston, IA 50131, USA
| | - Erik van Oosterom
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lucas Borras
- Corteva Agriscience, 8305 62nd Avenue, Johnston, IA 50131, USA
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia
| |
Collapse
|
7
|
Chen X, Huang Z, Fu D, Fang J, Zhang X, Feng X, Xie J, Wu B, Luo Y, Zhu M, Qi Y. Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2022; 13:841693. [PMID: 35693186 PMCID: PMC9185841 DOI: 10.3389/fpls.2022.841693] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/24/2022] [Indexed: 06/09/2023]
Abstract
Sugarcane (Saccharum spp.) is an efficient crop mainly used for sugar and bioethanol production. High yield and high sucrose of sugarcane are always the fundamental demands in sugarcane growth worldwide. Leaf angle and size of sugarcane can be attributed to planting density, which was associated with yield. In this study, we performed genome-wide association studies (GWAS) with a panel of 216 sugarcane core parents and their derived lines (natural population) to determine the genetic basis of leaf angle and key candidate genes with +2, +3, and +4 leaf at the seedling, elongation, and mature stages. A total of 288 significantly associated loci of sugarcane leaf angle at different developmental stages (eight phenotypes) were identified by GWAS with 4,027,298 high-quality SNP markers. Among them, one key locus and 11 loci were identified in all three stages and two stages, respectively. An InDel marker (SNP Ss6A_102766953) linked to narrow leaf angle was obtained. Overall, 4,089 genes were located in the confidence interval of significant loci, among which 3,892 genes were functionally annotated. Finally, 13 core parents and their derivatives tagged with SNPs were selected for marker-assisted selection (MAS). These candidate genes are mainly related to MYB transcription factors, auxin response factors, serine/threonine protein kinases, etc. They are directly or indirectly associated with leaf angle in sugarcane. This research provided a large number of novel genetic resources for the improvement of leaf angles and simultaneously to high yield and high bioethanol production.
Collapse
Affiliation(s)
- Xinglong Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Zhenghui Huang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Danwen Fu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Junteng Fang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiangbo Zhang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaomin Feng
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
| | - Jinfang Xie
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Bin Wu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yiji Luo
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Mingfeng Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongwen Qi
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| |
Collapse
|
8
|
Yin X, Gu J, Dingkuhn M, Struik PC. A model-guided holistic review of exploiting natural variation of photosynthesis traits in crop improvement. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3173-3188. [PMID: 35323898 PMCID: PMC9126731 DOI: 10.1093/jxb/erac109] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/22/2022] [Indexed: 05/18/2023]
Abstract
Breeding for improved leaf photosynthesis is considered as a viable approach to increase crop yield. Whether it should be improved in combination with other traits has not been assessed critically. Based on the quantitative crop model GECROS that interconnects various traits to crop productivity, we review natural variation in relevant traits, from biochemical aspects of leaf photosynthesis to morpho-physiological crop characteristics. While large phenotypic variations (sometimes >2-fold) for leaf photosynthesis and its underlying biochemical parameters were reported, few quantitative trait loci (QTL) were identified, accounting for a small percentage of phenotypic variation. More QTL were reported for sink size (that feeds back on photosynthesis) or morpho-physiological traits (that affect canopy productivity and duration), together explaining a much greater percentage of their phenotypic variation. Traits for both photosynthetic rate and sustaining it during grain filling were strongly related to nitrogen-related traits. Much of the molecular basis of known photosynthesis QTL thus resides in genes controlling photosynthesis indirectly. Simulation using GECROS demonstrated the overwhelming importance of electron transport parameters, compared with the maximum Rubisco activity that largely determines the commonly studied light-saturated photosynthetic rate. Exploiting photosynthetic natural variation might significantly improve crop yield if nitrogen uptake, sink capacity, and other morpho-physiological traits are co-selected synergistically.
Collapse
Affiliation(s)
- Xinyou Yin
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
- Correspondence:
| | - Junfei Gu
- College of Agriculture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | | | - Paul C Struik
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| |
Collapse
|
9
|
Cao Y, Zhong Z, Wang H, Shen R. Leaf angle: a target of genetic improvement in cereal crops tailored for high-density planting. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:426-436. [PMID: 35075761 PMCID: PMC8882799 DOI: 10.1111/pbi.13780] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 05/12/2023]
Abstract
High-density planting is an effective measure for increasing crop yield per unit land area. Leaf angle (LA) is a key trait of plant architecture and a target for genetic improvement of crops. Upright leaves allow better light capture in canopy under high-density planting, thus enhancing photosynthesis efficiency, ventilation and stress resistance, and ultimately higher grain yield. Here, we summarized the latest progress on the cellular and molecular mechanisms regulating LA formation in rice and maize. We suggest several standing out questions for future studies and then propose some promising strategies to manipulate LA for breeding of cereal crops tailored for high-density planting.
Collapse
Affiliation(s)
- Yingying Cao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Zhuojun Zhong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| |
Collapse
|
10
|
Peng B, Zhao X, Wang Y, Li C, Li Y, Zhang D, Shi Y, Song Y, Wang L, Li Y, Wang T. Genome-wide association studies of leaf angle in maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:50. [PMID: 37309541 PMCID: PMC10236034 DOI: 10.1007/s11032-021-01241-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/04/2021] [Indexed: 06/14/2023]
Abstract
Compact plant-type with small leaf angle has increased canopy light interception, which is conducive to the photosynthesis of the population and higher population yield at high density planting in maize. In this study, a panel of 285 diverse maize inbred lines genotyped with 56,000 SNPs was used to investigate the genetic basis of leaf angle across 3 consecutive years using a genome-wide association study (GWAS). The leaf angle showed broad phenotypic variation and high heritability across different years. Population structure analysis subdivided the panel into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Tangsipingtou, Reid, Lancaster and P. When tested with the optimal GWAS model, we found that the Q + K model was the best in reducing false positive. In total, 96 SNPs accounting for 5.54-10.44% of phenotypic variation were significantly (P < 0.0001) associated with leaf angle across three years. According to the linkage disequilibrium decay distance, 96 SNPs were binned into 43 QTLs for leaf angle. Seven major QTLs with R2 > 8% stably detected in at least 2 years, and BLUP values were clustered in four genomic regions (bins 2.01, 2.07, 5.06, and 10.04). Seven important candidate genes, Zm00001d001961, Zm00001d006348, Zm00001d006463, Zm00001d017618, Zm00001d024919, Zm00001d025018, and Zm00001d025033 were predicted for the seven stable major QTLs, respectively. The markers identified in this study can be used for molecular breeding for leaf angle, and the candidate genes would contribute to further understanding of the genetic basis of leaf angle. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01241-0.
Collapse
Affiliation(s)
- Bo Peng
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Xiaolei Zhao
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Yi Wang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lei Wang
- Handan Academy of Agricultural Sciences, Handan, 056001 Hebei China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| |
Collapse
|
11
|
Mei X, Nan J, Zhao Z, Yao S, Wang W, Yang Y, Bai Y, Dong E, Liu C, Cai Y. Maize transcription factor ZmNF-YC13 regulates plant architecture. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4757-4772. [PMID: 33831218 DOI: 10.1093/jxb/erab157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Leaf angle and leaf orientation value (LOV) are critical agronomic traits for maize plant architecture. The functions of NUCLEAR FACTOR Y (NF-Y) members in regulating plant architecture have not been reported yet. Here, we identified a regulator of maize plant architecture, NF-Y subunit C13 (ZmNF-YC13). ZmNF-YC13 was highly expressed in the leaf base zone of maize plants. ZmNF-YC13 overexpressing plants showed upright leaves with narrow leaf angle and larger LOV, while ZmNF-YC13 knockout plants had larger leaf angle and smaller LOV compared with wild-type plants. The changes in plant architecture were due to the changes in the expression of cytochrome P450 family members. ZmNF-YC13 interacts with two NF-Y subunit B members (ZmNF-YB9 and ZmNF-YB10) of the LEAFY COTYLEDON1 sub-family, and further recruits NF-Y subunit A (ZmNF-YA3) to form two NF-Y complexes. The two complexes can both activate the promoters of transcriptional repressors (ZmWRKY76 and ZmBT2), and the promoters of PLASTOCHRON group genes can be repressed by ZmWRKY76 and ZmBT2 in maize protoplasts. We propose that ZmNF-YC13 functions as a transcriptional regulator and, together with ZmNF-YBs and ZmNF-YA3, affects plant architecture by regulating the expression of ZmWRKY76 and ZmBT2, which repress the expression of cytochrome P450 family members in PLASTOCHRON branch.
Collapse
Affiliation(s)
- Xiupeng Mei
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Jin Nan
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Zikun Zhao
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Shun Yao
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Wenqin Wang
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Yang Yang
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Yang Bai
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Erfei Dong
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Chaoxian Liu
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| | - Yilin Cai
- Maize Research Institute, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Beibei District, Chongqing, People's Republic of China
| |
Collapse
|
12
|
Imran. The bioavailability of phosphorus in composite vs. hybrid maize differ with phosphorus and boron fertilization. PHOSPHORUS SULFUR 2021. [DOI: 10.1080/10426507.2021.1920588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Imran
- Department of Agronomy, The University of Agriculture, Peshawar, Pakistan
| |
Collapse
|
13
|
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
|
14
|
Dou D, Han S, Cao L, Ku L, Liu H, Su H, Ren Z, Zhang D, Zeng H, Dong Y, Liu Z, Zhu F, Zhao Q, Xie J, Liu Y, Cheng H, Chen Y. CLA4 regulates leaf angle through multiple hormone signaling pathways in maize. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1782-1794. [PMID: 33270106 DOI: 10.1093/jxb/eraa565] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Leaf angle is an important agronomic trait in cereals and shares a close relationship with crop architecture and grain yield. Although it has been previously reported that ZmCLA4 can influence leaf angle, the underlying mechanism remains unclear. In this study, we used the Gal4-LexA/UAS system and transactivation analysis to demonstrate in maize (Zea mays) that ZmCLA4 is a transcriptional repressor that regulates leaf angle. DNA affinity purification sequencing (DAP-Seq) analysis revealed that ZmCLA4 mainly binds to promoters containing the EAR motif (CACCGGAC) as well as to two other motifs (CCGARGS and CDTCNTC) to inhibit the expression of its target genes. Further analysis of ZmCLA4 target genes indicated that ZmCLA4 functions as a hub of multiple plant hormone signaling pathways: ZmCLA4 was found to directly bind to the promoters of multiple genes including ZmARF22 and ZmIAA26 in the auxin transport pathway, ZmBZR3 in the brassinosteroid signaling pathway, two ZmWRKY genes involved in abscisic acid metabolism, ZmCYP genes (ZmCYP75B1, ZmCYP93D1) related to jasmonic acid metabolism, and ZmABI3 involved in the ethylene response pathway. Overall, our work provides deep insights into the ZmCLA4 regulatory network in controlling leaf angle in maize.
Collapse
Affiliation(s)
- Dandan Dou
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Shengbo Han
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Liru Cao
- Henan Academy of Agricultural Science, Zhengzhou, Henan, China
| | - Lixia Ku
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Huafeng Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Huihui Su
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Zhenzhen Ren
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Dongling Zhang
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Haixia Zeng
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Yahui Dong
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Zhixie Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Fangfang Zhu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Qiannan Zhao
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Jiarong Xie
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Yajing Liu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Haiyang Cheng
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| | - Yanhui Chen
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengdong New Area, Zhengzhou, Henan, China
| |
Collapse
|
15
|
Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize. PLoS One 2021; 16:e0245129. [PMID: 33406127 PMCID: PMC7787474 DOI: 10.1371/journal.pone.0245129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/22/2020] [Indexed: 11/29/2022] Open
Abstract
Leaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed a F3:4 recombinant inbred lines (RIL) population to map QTL for leaf angle. The RIL was derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture. A sum of eight QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family (HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome re-sequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle. Besides, this will be helpful to develop the novel maize varieties with ideal plant architecture through marker-assisted selection.
Collapse
|
16
|
Ahn E, Odvody G, Prom LK, Magill C. Leaf angle distribution in Johnsongrass, leaf thickness in sorghum and Johnsongrass, and association with response to Colletotrichum sublineola. Sci Rep 2020; 10:22320. [PMID: 33339866 PMCID: PMC7749152 DOI: 10.1038/s41598-020-79473-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
Basal leaf angle distribution was surveyed in twenty-one Johnsongrass cultivars near the end of the vegetative stage. The angles increased from the top to the bottom leaves, and compared to cultivated grain sorghums, the average angle was larger in Johnsongrass. When basal leaf angle distribution data were correlated with pathogenicity test data from excised-leaf assays for three isolates of Colletotrichum sublineola, the results showed a weak positive correlation between basal leaf angle and pathogenicity level in Johnsongrass. In order to investigate a protective role of leaf thickness to C. sublineola, leaf thickness was measured in three sorghum cultivars and one Johnsongrass cultivar at the 8-leaf-stage. Leaf thickness near the apex, near the base, and half-way between the two points were measured in the top four leaves of each plant. Thickness of leaf blade and midrib were recorded separately. Using an excised-leaf-assay, the three points were inoculated with C. sublineola, and pathogenicity level was recorded 4-days-post-inoculation. Results showed strong negative correlations between leaf midrib thickness and pathogenicity level in sorghum and Johnsongrass but not in leaf blades.
Collapse
Affiliation(s)
- Ezekiel Ahn
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Gary Odvody
- Texas A&M AgriLife Research, Corpus Christi, TX, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
17
|
Maize Introgression Library Provides Evidence for the Involvement of liguleless1 in Resistance to Northern Leaf Blight. G3-GENES GENOMES GENETICS 2020; 10:3611-3622. [PMID: 32816917 PMCID: PMC7534436 DOI: 10.1534/g3.120.401500] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plant disease resistance is largely governed by complex genetic architecture. In maize, few disease resistance loci have been characterized. Near-isogenic lines are a powerful genetic tool to dissect quantitative trait loci. We analyzed an introgression library of maize (Zea mays) near-isogenic lines, termed a nested near-isogenic line library for resistance to northern leaf blight caused by the fungal pathogen Setosphaeria turcica The population was comprised of 412 BC5F4 near-isogenic lines that originated from 18 diverse donor parents and a common recurrent parent, B73. Single nucleotide polymorphisms identified through genotyping by sequencing were used to define introgressions and for association analysis. Near-isogenic lines that conferred resistance and susceptibility to northern leaf blight were comprised of introgressions that overlapped known northern leaf blight quantitative trait loci. Genome-wide association analysis and stepwise regression further resolved five quantitative trait loci regions, and implicated several candidate genes, including Liguleless1, a key determinant of leaf architecture in cereals. Two independently-derived mutant alleles of liguleless1 inoculated with S. turcica showed enhanced susceptibility to northern leaf blight. In the maize nested association mapping population, leaf angle was positively correlated with resistance to northern leaf blight in five recombinant inbred line populations, and negatively correlated with northern leaf blight in four recombinant inbred line populations. This study demonstrates the power of an introgression library combined with high density marker coverage to resolve quantitative trait loci. Furthermore, the role of liguleless1 in leaf architecture and in resistance to northern leaf blight has important applications in crop improvement.
Collapse
|
18
|
Kenchanmane Raju SK, Adkins M, Enersen A, Santana de Carvalho D, Studer AJ, Ganapathysubramanian B, Schnable PS, Schnable JC. Leaf Angle eXtractor: A high-throughput image processing framework for leaf angle measurements in maize and sorghum. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11385. [PMID: 32999772 PMCID: PMC7507698 DOI: 10.1002/aps3.11385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/17/2020] [Indexed: 05/08/2023]
Abstract
PREMISE Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment. METHODS High-throughput time series image data from water-deprived maize (Zea mays subsp. mays) and sorghum (Sorghum bicolor) were obtained using battery-powered time-lapse cameras. A MATLAB-based image processing framework, Leaf Angle eXtractor (LAX), was developed to extract and quantify leaf angles from images of maize and sorghum plants under drought conditions. RESULTS Leaf angle measurements showed differences in leaf responses to drought in maize and sorghum. Tracking leaf angle changes at intervals as short as one minute enabled distinguishing leaves that showed signs of wilting under water deprivation from other leaves on the same plant that did not show wilting during the same time period. DISCUSSION Automating leaf angle measurements using LAX makes it feasible to perform large-scale experiments to evaluate, understand, and exploit the spatial and temporal variations in plant response to water limitations.
Collapse
Affiliation(s)
- Sunil K. Kenchanmane Raju
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Present address:
Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Miles Adkins
- Department of Mechanical EngineeringIowa State UniversityAmesIowaUSA
| | - Alex Enersen
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
| | - Daniel Santana de Carvalho
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Present address:
Department of BioinformaticsFederal University of Minas GeraisBelo HorizonteMinas GeraisBrazil
| | | | | | | | - James C. Schnable
- Center for Plant Science InnovationUniversity of Nebraska–LincolnLincolnNebraskaUSA
- Department of Agronomy and HorticultureUniversity of Nebraska–LincolnLincolnNebraskaUSA
| |
Collapse
|
19
|
Synergistic Interaction of Phytohormones in Determining Leaf Angle in Crops. Int J Mol Sci 2020; 21:ijms21145052. [PMID: 32709150 PMCID: PMC7404121 DOI: 10.3390/ijms21145052] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Leaf angle (LA), defined as the angle between the plant stem and leaf adaxial side of the blade, generally shapes the plant architecture into a loosen or dense structure, and thus influences the light interception and competition between neighboring plants in natural settings, ultimately contributing to the crop yield and productivity. It has been elucidated that brassinosteroid (BR) plays a dominant role in determining LA, and other phytohormones also positively or negatively participate in regulating LA. Accumulating evidences have revealed that these phytohormones interact with each other in modulating various biological processes. However, the comprehensive discussion of how the phytohormones and their interaction involved in shaping LA is relatively lack. Here, we intend to summarize the advances in the LA regulation mediated by the phytohormones and their crosstalk in different plant species, mainly in rice and maize, hopefully providing further insights into the genetic manipulation of LA trait in crop breeding and improvement in regarding to overcoming the challenge from the continuous demands for food under limited arable land area.
Collapse
|
20
|
Dzievit MJ, Li X, Yu J. Dissection of Leaf Angle Variation in Maize through Genetic Mapping and Meta-Analysis. THE PLANT GENOME 2019; 12:180024. [PMID: 30951086 DOI: 10.3835/plantgenome2018.05.0024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Maize ( L.) hybrids have transitioned to upright leaf angles (LAs) over the last 50 yr as maize yields and planting densities increased concurrently. Genetic mapping and a meta-analysis were conducted in the present study to dissect genetic factors controlling LA variation. We developed mapping populations using inbred lines B73 (Iowa Stiff Stalk Synthetic), PHW30 (Iodent, expired plant variety protection inbred), and Mo17 (Non-Stiff Stalk) that have distinct LA architectures and represent three important heterotic groups in the United States. These populations were genotyped using genotyping-by-sequencing (GBS), and phenotyped for LA in the F and F generation. Inclusive composite interval mapping across the two generations of the mapping populations revealed 12 quantitative trait loci (QTL), and a consistent QTL on chromosome 1 explained 10 to 17% of the phenotypic variance. To gain a comprehensive understanding of natural variations underlying LA variation, these detected QTL were compared with results from 19 previous studies. In total, 495 QTL were compiled and mapped into 143 genomic bins. A meta-analysis revealed that 58 genomic bins were associated with LA variation. Thirty-three candidate genes were identified in these genomic bins. Together, these results provide evidence of QTL controlling LA variation from inbred lines representing three important heterotic groups in the United States and a useful resource for future research into the molecular variants underlying specific regions of the genome associated with LA variation.
Collapse
|
21
|
Zhao Y, Wang H, Bo C, Dai W, Zhang X, Cai R, Gu L, Ma Q, Jiang H, Zhu J, Cheng B. Genome-wide association study of maize plant architecture using F 1 populations. PLANT MOLECULAR BIOLOGY 2019; 99:1-15. [PMID: 30519826 DOI: 10.1007/s11103-018-0797-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 11/10/2018] [Indexed: 06/09/2023]
Abstract
Genome-wide association study of maize plant architecture using F1 populations can better dissect various genetic effects that can provide precise guidance for genetic improvement in maize breeding. Maize grain yield has increased at least eightfold during the past decades. Plant architecture, including plant height, leaf angle, leaf length, and leaf width, has been changed significantly to adapt to higher planting density. Although the genetic architecture of these traits has been dissected using different populations, the genetic basis remains unclear in the F1 population. In this work, we perform a genome-wide association study of the four traits using 573 F1 hybrids with a mixed linear model approach and QTXNetwork mapping software. A total of 36 highly significant associated quantitative trait SNPs were identified for these traits, which explained 51.86-79.92% of the phenotypic variation and were contributed mainly by additive, dominance, and environment-specific effects. Heritability as a result of environmental interaction was more important for leaf angle and leaf length, while major effects (a, aa, and d) were more important for leaf width and plant height. The potential breeding values of the superior lines and superior hybrids were also predicted, and these values can be applied in maize breeding by direct selection of superior genotypes for the associated quantitative trait SNPs. A total of 108 candidate genes were identified for the four traits, and further analysis was performed to screen the potential genes involved in the development of maize plant architecture. Our results provide new insights into the genetic architecture of the four traits, and will be helpful in marker-assisted breeding for maize plant architecture.
Collapse
Affiliation(s)
- Yang Zhao
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Hengsheng Wang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Chen Bo
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Wei Dai
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xingen Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Longjiang Gu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Haiyang Jiang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Jun Zhu
- Institute of Bioinformatics, Zhejiang University, Hangzhou, China.
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China.
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, China.
| |
Collapse
|
22
|
Comparative mapping of quantitative trait loci for tassel-related traits of maize in $$\hbox {F}_{2:3}$$ F 2 : 3 and RIL populations. J Genet 2018. [DOI: 10.1007/s12041-018-0908-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
23
|
Yi Q, Liu Y, Zhang X, Hou X, Zhang J, Liu H, Hu Y, Yu G, Huang Y. Comparative mapping of quantitative trait loci for tassel-related traits of maize in F 2:3 and RIL populations. J Genet 2018; 97:253-266. [PMID: 29666344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tassel architecture is an important trait in maize breeding and hybrid seed production. In this study, we investigated total tassel length (TTL) and tassel branch number (TBN) in 266 F2:3 families across six environments and in 301 recombinant inbred lines (RILs) across three environments, where all the plants were derived from a cross between 08-641 and Ye478. We compared the genetic architecture of the two traits across two generations through combined analysis. In total, 27 quantitative trait loci (QTLs) (15 in F2:3; 16 in RIL), two QTL × environment interactions (both in F2:3), 11 pairs of epistatic interactions (seven in F2:3; four in RIL) and four stable QTLs in both the F2:3 and RILs were detected. The RIL population had higher detection power than the F2:3 population. Nevertheless, QTL × environment interactions and epistatic interactions could be more easily detected in the F2:3 population than in the RILs. Overall, the QTL mapping results in the F2:3 and RILs were greatly influenced by genetic generations and environments. Finally, fine mapping for a novel and major QTL, qTTL-2-3 (bin 2.07), which accounted for over 8.49% of the phenotypic variation across different environments and generations, could be useful in marker-assisted breeding.
Collapse
Affiliation(s)
- Qiang Yi
- Agronomy College, Sichuan Agricultural University, Chengdu 611130, Sichuan, People's Republic of China.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Liu R, Meng Q, Zheng F, Kong L, Yuan J, Lübberstedt T. Genetic mapping of QTL for maize leaf width combining RIL and IF2 populations. PLoS One 2017; 12:e0189441. [PMID: 29232707 PMCID: PMC5726739 DOI: 10.1371/journal.pone.0189441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/24/2017] [Indexed: 01/01/2023] Open
Abstract
Leaf width is an important component of plant architecture that affects light capture during photosynthesis and wind circulation under dense planting conditions. To improve understanding of the genetic mechanisms involved in leaf width at different positions, a comprehensive evaluation using the RIL (Recombinant Inbred Line) and IF2 (Immortalized F2) populations and a subsequent meta-analysis were performed. Forty-seven QTL associated with leaf width at different positions below the tassel were detected. The individual effects of QTL explained 3.5% to 17.0% of the observed phenotypic variation, and ten QTL explained over 10%. The initial QTL were integrated into eight mQTL (meta-QTL) through a meta-analysis. Our results suggested that leaf widths at different positions may be affected by several of the same mQTL and may also be regulated by many different mQTL. These results provide useful information for breeding high density tolerant inbred lines and hybrid cultivars, as well as for using marker-assisted selection for important mQTL.
Collapse
Affiliation(s)
- Ruixiang Liu
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Qingchang Meng
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Fei Zheng
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Lingjie Kong
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Jianhua Yuan
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Ames, Iowa State, United States of America
| |
Collapse
|
25
|
QTL analysis of ear leaf traits in maize ( Zea mays L.) under different planting densities. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.cj.2017.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
26
|
Liu C, Zhou Q, Dong L, Wang H, Liu F, Weng J, Li X, Xie C. Genetic architecture of the maize kernel row number revealed by combining QTL mapping using a high-density genetic map and bulked segregant RNA sequencing. BMC Genomics 2016; 17:915. [PMID: 27842488 PMCID: PMC5109822 DOI: 10.1186/s12864-016-3240-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/01/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The maize kernel row number (KRN) is a key component that contributes to grain yield and has high broad-sense heritability (H 2 ). Quantitative trait locus/loci (QTL) mapping using a high-density genetic map is a powerful approach to detecting loci that are responsible for traits of interest. Bulked segregant ribonucleic acid (RNA) sequencing (BSR-seq) is another rapid and cost-effective strategy to identify QTL. Combining QTL mapping using a high-density genetic map and BSR-seq may dissect comprehensively the genetic architecture underlying the maize KRN. RESULTS A panel of 300 F2 individuals derived from inbred lines abe2 and B73 were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 4,579 high-quality polymorphic SLAF markers were obtained and used to construct a high-density genetic map with a total length of 2,123 centimorgan (cM) and an average distance between adjacent markers of 0.46 cM. Combining the genetic map and KRN of F2 individuals, four QTL (qKRN1, qKRN2, qKRN5, and qKRN8-1) were identified on chromosomes 1, 2, 5, and 8, respectively. The physical intervals of these four QTL ranged from 4.36 Mb for qKRN8-1 to 7.11 Mb for qKRN1 with an average value of 6.08 Mb. Based on high-throughput sequencing of two RNA pools bulked from leaves of plants with extremely high and low KRNs, two QTL were detected on chromosome 8 in the 10-25 Mb (BSR_QTL1) and 60-150 Mb (BSR_QTL2) intervals. According to the physical positions of these QTL, qKRN8-1 was included by BSR_QTL2. In addition, qKRN8-1 was validated using QTL mapping with a recombinant inbred lines population that was derived from inbred lines abe2 and B73. CONCLUSIONS In this study, we proved that combining QTL mapping using a high-density genetic map and BSR-seq is a powerful and cost-effective approach to comprehensively revealing genetic architecture underlying traits of interest. The QTL for the KRN detected in this study, especially qKRN8-1, can be used for performing fine mapping experiments and marker-assisted selection in maize breeding.
Collapse
Affiliation(s)
- Changlin Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Qiang Zhou
- Anhui Agricultural University, Hefei, Anhui Province, 230036, China
| | - Le Dong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Hui Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Fang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| |
Collapse
|
27
|
Yang C, Tang D, Qu J, Zhang L, Zhang L, Chen Z, Liu J. Genetic mapping of QTL for the sizes of eight consecutive leaves below the tassel in maize (Zea mays L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2191-2209. [PMID: 27550554 DOI: 10.1007/s00122-016-2767-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 08/12/2016] [Indexed: 05/18/2023]
Abstract
A set of RIL population was used to detect QTL associated with the sizes of eight consecutive leaves, across different environments, and ten QTL clusters were identified as main QTLs. One of the important parameters of the maize leaf architecture that affects light penetration into the canopy, leaf size, has long attracted breeders' attention for optimizing the plant type of maize and for maximizing the grain yield (GY). In this study, we used 253 RIL lines derived from a cross between B73 and SICAU1212 to investigate the leaf widths (LWs), leaf lengths (LLs), and leaf areas (LAs) of eight consecutive leaves of maize below the tassel and GY across different environments and to identify quantitative traits loci (QTLs) controlling the above-mentioned traits, using inclusive interval mapping for single-environment analysis plus a mixed-model-based composite interval mapping for joint analysis. A total of 171 and 159 putative QTLs were detected through these two mapping methods, respectively. Single-environment mapping revealed that 39 stable QTLs explained more than 10 % of the phenotypic variance, and 35 of the 39 QTLs were also detected by joint analysis. In addition, joint analysis showed that nine of the 159 QTLs exhibited significant QTL × environment interaction and 15 significant epistatic interactions were identified. Approximately 47.17 % of the QTLs for leaf architectural traits in joint analysis were concentrated in ten main chromosomal regions, namely, bins 1.07, 2.02, 3.06, 4.09, 5.01, 5.02, 5.03-5.04, 5.07, 6.07, and 8.05. This study should provide a basis for further fine-mapping of these main genetic regions and improvement of maize leaf architecture.
Collapse
Affiliation(s)
- Cong Yang
- Maize Research, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
| | - Dengguo Tang
- Maize Research, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Jingtao Qu
- Maize Research, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Ling Zhang
- Maize Research, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Lei Zhang
- Maize Research, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Zhengjie Chen
- Maize Research, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Jian Liu
- Maize Research, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
| |
Collapse
|
28
|
Perez RPA, Pallas B, Le Moguédec G, Rey H, Griffon S, Caliman JP, Costes E, Dauzat J. Integrating mixed-effect models into an architectural plant model to simulate inter- and intra-progeny variability: a case study on oil palm (Elaeis guineensis Jacq.). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4507-21. [PMID: 27302128 DOI: 10.1093/jxb/erw203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Three-dimensional (3D) reconstruction of plants is time-consuming and involves considerable levels of data acquisition. This is possibly one reason why the integration of genetic variability into 3D architectural models has so far been largely overlooked. In this study, an allometry-based approach was developed to account for architectural variability in 3D architectural models of oil palm (Elaeis guineensis Jacq.) as a case study. Allometric relationships were used to model architectural traits from individual leaflets to the entire crown while accounting for ontogenetic and morphogenetic gradients. Inter- and intra-progeny variabilities were evaluated for each trait and mixed-effect models were used to estimate the mean and variance parameters required for complete 3D virtual plants. Significant differences in leaf geometry (petiole length, density of leaflets, and rachis curvature) and leaflet morphology (gradients of leaflet length and width) were detected between and within progenies and were modelled in order to generate populations of plants that were consistent with the observed populations. The application of mixed-effect models on allometric relationships highlighted an interesting trade-off between model accuracy and ease of defining parameters for the 3D reconstruction of plants while at the same time integrating their observed variability. Future research will be dedicated to sensitivity analyses coupling the structural model presented here with a radiative balance model in order to identify the key architectural traits involved in light interception efficiency.
Collapse
Affiliation(s)
| | - Benoît Pallas
- INRA, UMR 1334 AGAP, 34398 Montpellier Cedex 5, France
| | | | - Hervé Rey
- CIRAD, UMR AMAP, Montpellier, F-34000 France
| | | | | | | | - Jean Dauzat
- CIRAD, UMR AMAP, Montpellier, F-34000 France
| |
Collapse
|
29
|
Chen L, Li YX, Li C, Wu X, Qin W, Li X, Jiao F, Zhang X, Zhang D, Shi Y, Song Y, Li Y, Wang T. Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize. BMC PLANT BIOLOGY 2016; 16:81. [PMID: 27068015 PMCID: PMC4828868 DOI: 10.1186/s12870-016-0768-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/06/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs. qGW4.05 is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at qGW4.05. RESULTS QTL qGW4.05 was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for qGW4.05. Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size. CONCLUSION The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for qGW4.05. These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.
Collapse
Affiliation(s)
- Lin Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Yong-xiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Chunhui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Xun Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Weiwei Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Xin Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Fuchao Jiao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Xiaojing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Dengfeng Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Yunsu Shi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Yanchun Song
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| | - Tianyu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081 China
| |
Collapse
|
30
|
Meng Y, Li J, Liu J, Hu H, Li W, Liu W, Chen S. Ploidy effect and genetic architecture exploration of stalk traits using DH and its corresponding haploid populations in maize. BMC PLANT BIOLOGY 2016; 16:50. [PMID: 26911156 PMCID: PMC4766647 DOI: 10.1186/s12870-016-0742-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/18/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Doubled haploid (DH) lines produced via in vivo haploid induction have become indispensable in maize research and practical breeding, so it is important to understand traits characteristics in DH and its corresponding haploids which derived from each DH lines. In this study, a DH population derived from Zheng58 × Chang7-2 and a haploid population, were developed, genotyped and evaluated to investigate genetic architecture of eight stalk traits, especially rind penetrometer resistance (RPR) and in vitro dry matter digestion (IVDMD), which affecting maize stalk lodging-resistance and feeding values, respectively. RESULTS Phenotypic correlation coefficients ranged from 0.38 to 0.69 between the two populations for eight stalk traits. Heritability values of all stalk traits ranged from 0.49 to 0.81 in the DH population, and 0.58 to 0.89 in the haploid population. Quantitative trait loci (QTL) mapping study showed that a total of 47 QTL for all traits accounting for genetic variations ranging from 1.6 to 36.5% were detected in two populations. One or more QTL sharing common region for each trait were detected between two different ploidy populations. Potential candidate genes predicated from the four QTL support intervals for RPR and IVDMD were indirectly or directly involved with cellulose and lignin biosynthesis, which participated in cell wall formation. The increased expression levels of lignin and cellulose synthesis key genes in the haploid situation illustrated that dosage compensation may account for genome dosage effect in our study. CONCLUSIONS The current investigation extended understanding about the genetic basis of stalk traits and correlations between DH and its haploid populations, which showed consistence and difference between them in phenotype, QTL characters, and gene expression. The higher heritabilities and partly higher QTL detection power were presented in haploid population than in DH population. All of which described above could lay a preliminary foundation for genetic architecture study with haploid population and may benefit selection in haploid-stage to reduce cost in DH breeding.
Collapse
Affiliation(s)
- Yujie Meng
- National Maize Improvement Center of China, China Agricultural University (West Campus), 2# Yuanmingyuan West Road, Beijing, 100193, China.
| | - Junhui Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy, China Agricultural University (West Campus), 2# Yuanmingyuan West Road, Beijing, 100193, China.
| | - Jianju Liu
- National Maize Improvement Center of China, China Agricultural University (West Campus), 2# Yuanmingyuan West Road, Beijing, 100193, China.
| | - Haixiao Hu
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany.
| | - Wei Li
- National Maize Improvement Center of China, China Agricultural University (West Campus), 2# Yuanmingyuan West Road, Beijing, 100193, China.
| | - Wenxin Liu
- National Maize Improvement Center of China, China Agricultural University (West Campus), 2# Yuanmingyuan West Road, Beijing, 100193, China.
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy, China Agricultural University (West Campus), 2# Yuanmingyuan West Road, Beijing, 100193, China.
| | - Shaojiang Chen
- National Maize Improvement Center of China, China Agricultural University (West Campus), 2# Yuanmingyuan West Road, Beijing, 100193, China.
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy, China Agricultural University (West Campus), 2# Yuanmingyuan West Road, Beijing, 100193, China.
| |
Collapse
|
31
|
Truong SK, McCormick RF, Rooney WL, Mullet JE. Harnessing Genetic Variation in Leaf Angle to Increase Productivity of Sorghum bicolor. Genetics 2015; 201:1229-38. [PMID: 26323882 PMCID: PMC4649647 DOI: 10.1534/genetics.115.178608] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/28/2015] [Indexed: 12/22/2022] Open
Abstract
The efficiency with which a plant intercepts solar radiation is determined primarily by its architecture. Understanding the genetic regulation of plant architecture and how changes in architecture affect performance can be used to improve plant productivity. Leaf inclination angle, the angle at which a leaf emerges with respect to the stem, is a feature of plant architecture that influences how a plant canopy intercepts solar radiation. Here we identify extensive genetic variation for leaf inclination angle in the crop plant Sorghum bicolor, a C4 grass species used for the production of grain, forage, and bioenergy. Multiple genetic loci that regulate leaf inclination angle were identified in recombinant inbred line populations of grain and bioenergy sorghum. Alleles of sorghum dwarf-3, a gene encoding a P-glycoprotein involved in polar auxin transport, are shown to change leaf inclination angle by up to 34° (0.59 rad). The impact of heritable variation in leaf inclination angle on light interception in sorghum canopies was assessed using functional-structural plant models and field experiments. Smaller leaf inclination angles caused solar radiation to penetrate deeper into the canopy, and the resulting redistribution of light is predicted to increase the biomass yield potential of bioenergy sorghum by at least 3%. These results show that sorghum leaf angle is a heritable trait regulated by multiple loci and that genetic variation in leaf angle can be used to modify plant architecture to improve sorghum crop performance.
Collapse
Affiliation(s)
- Sandra K Truong
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843 Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
| | - Ryan F McCormick
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843 Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
| | - William L Rooney
- Soil and Crop Sciences Department, Texas A&M University, College Station, Texas 77843
| | - John E Mullet
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843 Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
32
|
Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population. PLoS One 2015; 10:e0141619. [PMID: 26509792 PMCID: PMC4625009 DOI: 10.1371/journal.pone.0141619] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/09/2015] [Indexed: 11/19/2022] Open
Abstract
Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.
Collapse
|
33
|
Differences in properties and proteomes of the midribs contribute to the size of the leaf angle in two near-isogenic maize lines. J Proteomics 2015; 128:113-22. [PMID: 26244907 DOI: 10.1016/j.jprot.2015.07.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/16/2015] [Accepted: 07/23/2015] [Indexed: 12/23/2022]
Abstract
The midrib of maize leaves provides the primary support for the blade and is largely associated with leaf angle size. To elucidate the role of the midrib in leaf angle formation, the maize line Shen137 (larger leaf angle) and a near isogenic line (NIL, smaller leaf angle) were used in the present study. The results of the analysis showed that both the puncture forces and proximal collenchyma number of the midribs of the first and second leaves above the ear were higher in NIL than in Shen137. Comparative proteomic analysis was performed to reveal protein profile differences in the midribs of the 5th, 10th and 19th newly expanded leaves between Shen137 and NIL. Quantitative analysis of 24 identified midrib proteins indicated that the maximum changes in abundance of 22 proteins between Shen137 and NIL appeared at the 10th leaf stage, of which phosphoglycerate kinase, adenosine kinase, fructose-bisphosphate aldolase and adenylate kinase were implicated in glycometabolism. Thus, glycometabolism might be associated with leaf angle formation and the physical and mechanical properties of the midribs. These results provide insight into the mechanism underlying maize leaf angle formation.
Collapse
|
34
|
Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing. G3-GENES GENOMES GENETICS 2015; 5:1463-72. [PMID: 26044731 PMCID: PMC4502380 DOI: 10.1534/g3.115.017905] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis.
Collapse
|
35
|
Gong F, Wu X, Zhang H, Chen Y, Wang W. Making better maize plants for sustainable grain production in a changing climate. FRONTIERS IN PLANT SCIENCE 2015; 6:835. [PMID: 26500671 PMCID: PMC4593952 DOI: 10.3389/fpls.2015.00835] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/23/2015] [Indexed: 05/20/2023]
Abstract
Achieving grain supply security with limited arable land is a major challenge in the twenty-first century, owing to the changing climate and increasing global population. Maize plays an increasingly vital role in global grain production. As a C4 plant, maize has a high yield potential. Maize is predicted to become the number one cereal in the world by 2020. However, maize production has plateaued in many countries, and hybrid and production technologies have been fully exploited. Thus, there is an urgent need to shape maize traits and architectures for increased stress tolerance and higher yield in a changing climate. Recent achievements in genomics, proteomics, and metabolomics have provided an unprecedented opportunity to make better maize. In this paper, we discuss the current challenges and potential of maize production, particularly in China. We also highlight the need for enhancing maize tolerance to drought and heat waves, summarize the elite shoot and root traits and phenotypes, and propose an ideotype for sustainable maize production in a changing climate. This will facilitate targeted maize improvement through a conventional breeding program combined with molecular techniques.
Collapse
Affiliation(s)
| | | | | | | | - Wei Wang
- *Correspondence: Wei Wang, State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China,
| |
Collapse
|