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Tian Z, Wang X, Dun X, Zhao K, Wang H, Ren L. An integrated QTL mapping and transcriptome sequencing provides further molecular insights and candidate genes for stem strength in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:38. [PMID: 38294547 DOI: 10.1007/s00122-023-04535-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE We detected the major QTL- qSR.A07, which regulated stem strength and was fine-mapped to 490 kb. BnaA07G0302800ZS and BnaA07G0305700ZS as the candidate functional genes were identified at qSR.A07 locus. The stem's mechanical properties reflect its ability to resist lodging. In rapeseed (Brassica napus L.), although stem lodging negatively affects yield and generates harvesting difficulties, the molecular regulation of stem strength remains elusive. Hence, this study aimed to unravel the main loci and molecular mechanisms governing rapeseed stem strength. A mapping population consisting of 267 RILs (recombinant inbred lines) was developed from the crossed between ZS11 (high stem strength) and 4D122 (low stem strength), and two mechanical properties of stems including stem breaking strength and stem rind penetrometer resistance were phenotyped in four different environments. Four pleiotropic QTLs that were stable in at least two environments were detected. qSR.A07, the major one, was fine-mapped to a 490 kb interval between markers SA7-2711 and SA7-2760 on chromosome 7. It displayed epistatic interaction with qRPR.A09-2. Comparative transcriptome sequencing and analysis unveiled methionine/S-adenosylmethionine cycle (Met/SAM cycle), cytoskeleton organization, sulfur metabolism and phenylpropanoid biosynthesis as the main pathways associated with high stem strength. Further, we identified two candidate genes, BnaA07G0302800ZS and BnaA07G0305700ZS, at qSR.A07 locus. Gene sequence alignment identified a number of InDels, SNPs and amino acid variants in sequences of these genes between ZS11 and 4D122. Finally, based on these genetic variants, we developed three SNP markers of these genes to facilitate future genetic selection and functional studies. These findings offer important genetic resources for the molecular-assisted breeding of novel rapeseed stem lodging-resistant varieties.
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Affiliation(s)
- Zhengshu Tian
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Kaiqin Zhao
- Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Lijun Ren
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'An, China.
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Ma F, Shen Y, Su D, Adnan M, Wang M, Jiang F, Hu Q, Chen X, He G, Yao W, Zhang M, Huang J. A high-throughput phenotyping assay for precisely determining stalk crushing strength in large-scale sugarcane germplasm. FRONTIERS IN PLANT SCIENCE 2023; 14:1224268. [PMID: 37546250 PMCID: PMC10399216 DOI: 10.3389/fpls.2023.1224268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023]
Abstract
Sugarcane is a major industrial crop around the world. Lodging due to weak mechanical strength is one of the main problems leading to huge yield losses in sugarcane. However, due to the lack of high efficiency phenotyping methods for stalk mechanical strength characterization, genetic approaches for lodging-resistant improvement are severely restricted. This study attempted to apply near-infrared spectroscopy high-throughput assays for the first time to estimate the crushing strength of sugarcane stalks. A total of 335 sugarcane samples with huge variation in stalk crushing strength were collected for online NIRS modeling. A comprehensive analysis demonstrated that the calibration and validation sets were comparable. By applying a modified partial least squares method, we obtained high-performance equations that had large coefficients of determination (R2 > 0.80) and high ratio performance deviations (RPD > 2.4). Particularly, when the calibration and external validation sets combined for an integrative modeling, we obtained the final equation with a coefficient of determination (R2) and ratio performance deviation (RPD) above 0.9 and 3.0, respectively, demonstrating excellent prediction capacity. Additionally, the obtained model was applied for characterization of stalk crushing strength in large-scale sugarcane germplasm. In a three-year study, the genetic characteristics of stalk crushing strength were found to remain stable, and the optimal sugarcane genotypes were screened out consistently. In conclusion, this study offers a feasible option for a high-throughput analysis of sugarcane mechanical strength, which can be used for the breeding of lodging resistant sugarcane and beyond.
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Affiliation(s)
- Fumin Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Yinjuan Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
- Guangxi China-ASEAN Youth Industrial Park, Chongzuo Agricultural Hi-tech Industry Demo Zone, Chongzuo, Guangxi, China
| | - De Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Muhammad Adnan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Maoyao Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Fuhong Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Qian Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Xiaoru Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Guanyong He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Wei Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Jiangfeng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Ministry Co-sponsored Collaborative Innovation Center of Canesugar Industry, Academy of Sugarcane and Sugar Industry, College of Agriculture, Guangxi University, Nanning, Guangxi, China
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3
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Dai W, Yu H, Liu K, Chengxu Y, Yan J, Zhang C, Xi N, Liu H, Xiangchen C, Zou C, Zhang M, Gao S, Pan G, Ma L, Shen Y. Combined linkage mapping and association analysis uncovers candidate genes for 25 leaf-related traits across three environments in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:12. [PMID: 36662253 DOI: 10.1007/s00122-023-04285-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Combined linkage and association analysis revealed five co-localized genetic loci across multiple environments. The key gene Zm00001d026491 was further verified to influence leaf length by candidate gene association analysis. Leaf morphology and number determine the canopy structure and thus affect crop yield. Herein, the genetic basis and key genes for 25 leaf-related traits, including leaf lengths (LL), leaf widths (LW), and leaf areas (LA) of eight continuous leaves under the tassel, and the number of leaves above the primary ear (LAE), were dissected by using an association panel and a biparental population. Using an intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, 290 quantitative trait loci (QTL) controlling these traits were detected across different locations, among which 115 QTL were individually repeatedly identified in at least two environments. Using the association panel, 165 unique significant single-nucleotide polymorphisms (SNPs) were associated with target traits (P < 2.15E-06), of which 35 were separately detected across multiple environments. In total, 42 pleiotropic QTL/SNPs (pQTL/SNPs) were responsible for at least two of the LL, LW, LA, and LAE traits across multiple environments. Combining the QTL mapping and association study, five unique SNPs were located within the confidence intervals of seven QTL, and 77 genes were identified based on the linkage disequilibrium regions of co-localized SNP loci. Gene-based association studies verified that the intragenic variants in the candidate gene Zm00001d026491 influenced LL of the third leaf counted from the top node. These findings will provide vital information to understanding the genetic basis of leaf-related traits and help to cultivate maize varieties with ideal plant architecture.
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Affiliation(s)
- Wei Dai
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hong Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yujuan Chengxu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaquan Yan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Na Xi
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hao Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoyang Xiangchen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minyan Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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4
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Wu L, Zheng Y, Jiao F, Wang M, Zhang J, Zhang Z, Huang Y, Jia X, Zhu L, Zhao Y, Guo J, Chen J. Identification of quantitative trait loci for related traits of stalk lodging resistance using genome-wide association studies in maize (Zea mays L.). BMC Genom Data 2022; 23:76. [PMID: 36319954 PMCID: PMC9623923 DOI: 10.1186/s12863-022-01091-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 10/10/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Stalk lodging is one of the main factors affecting maize (Zea mays L.) yield and limiting mechanized harvesting. Developing maize varieties with high stalk lodging resistance requires exploring the genetic basis of lodging resistance-associated agronomic traits. Stalk strength is an important indicator to evaluate maize lodging and can be evaluated by measuring stalk rind penetrometer resistance (RPR) and stalk buckling strength (SBS). Along with morphological traits of the stalk for the third internodes length (TIL), fourth internode length (FIL), third internode diameter (TID), and the fourth internode diameter (FID) traits are associated with stalk lodging resistance. RESULTS In this study, a natural population containing 248 diverse maize inbred lines genotyped with 83,057 single nucleotide polymorphism (SNP) markers was used for genome-wide association study (GWAS) for six stalk lodging resistance-related traits. The heritability of all traits ranged from 0.59 to 0.72 in the association mapping panel. A total of 85 significant SNPs were identified for the association mapping panel using best linear unbiased prediction (BLUP) values of all traits. Additionally, five candidate genes were associated with stalk strength traits, which were either directly or indirectly associated with cell wall components. CONCLUSIONS These findings contribute to our understanding of the genetic basis of maize stalk lodging and provide valuable theoretical guidance for lodging resistance in maize breeding in the future.
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Affiliation(s)
- Lifen Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yunxiao Zheng
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Fuchao Jiao
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
| | - Ming Wang
- grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
| | - Jing Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Zhongqin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yaqun Huang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Xiaoyan Jia
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Liying Zhu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Yongfeng Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Jinjie Guo
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China
| | - Jingtang Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Hebei, Baoding 071001 China ,grid.412608.90000 0000 9526 6338College of Agronomy, Qingdao Agricultural University, Shandong, Qingdao 266109 China
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5
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Fei X, Wang Y, Zheng Y, Shen X, E L, Ding J, Lai J, Song W, Zhao H. Identification of two new QTLs of maize (Zea mays L.) underlying kernel row number using the HNAU-NAM1 population. BMC Genomics 2022; 23:593. [PMID: 35971070 PMCID: PMC9380338 DOI: 10.1186/s12864-022-08793-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maize kernel row number (KRN) is one of the most important yield traits and has changed greatly during maize domestication and selection. Elucidating the genetic basis of KRN will be helpful to improve grain yield in maize. RESULTS Here, we measured KRN in four environments using a nested association mapping (NAM) population named HNAU-NAM1 with 1,617 recombinant inbred lines (RILs) that were derived from 12 maize inbred lines with a common parent, GEMS41. Then, five consensus quantitative trait loci (QTLs) distributing on four chromosomes were identified in at least three environments along with the best linear unbiased prediction (BLUP) values by the joint linkage mapping (JLM) method. These QTLs were further validated by the separate linkage mapping (SLM) and genome-wide association study (GWAS) methods. Three KRN genes cloned through the QTL assay were found in three of the five consensus QTLs, including qKRN1.1, qKRN2.1 and qKRN4.1. Two new QTLs of KRN, qKRN4.2 and qKRN9.1, were also identified. On the basis of public RNA-seq and genome annotation data, five genes highly expressed in ear tissue were considered candidate genes contributing to KRN. CONCLUSIONS This study carried out a comprehensive analysis of the genetic architecture of KRN by using a new NAM population under multiple environments. The present results provide solid information for understanding the genetic components underlying KRN and candidate genes in qKRN4.2 and qKRN9.1. Single-nucleotide polymorphisms (SNPs) closely linked to qKRN4.2 and qKRN9.1 could be used to improve inbred yield during molecular breeding in maize.
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Affiliation(s)
- Xiaohong Fei
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.,Longping Agriculture Science Co. Ltd, Beijing, 100004, People's Republic of China
| | - Yifei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunxiao Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xiaomeng Shen
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lizhu E
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Junqiang Ding
- State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China. .,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Haiming Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China. .,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.
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6
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Liu J, Sun C, Guo S, Yin X, Yuan Y, Fan B, Lv Q, Cai X, Zhong Y, Xia Y, Dong X, Guo Z, Song G, Huang W. Genomic and Transcriptomic Analyses Reveal Pathways and Genes Associated With Brittle Stalk Phenotype in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:849421. [PMID: 35548303 PMCID: PMC9083323 DOI: 10.3389/fpls.2022.849421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The mechanical strength of the stalk affects the lodging resistance and digestibility of the stalk in maize. The molecular mechanisms regulating the brittleness of stalks in maize remain undefined. In this study, we constructed the maize brittle stalk mutant (bk5) by crossing the W22:Mu line with the Zheng 58 line. The brittle phenotype of the mutant bk5 existed in all of the plant organs after the five-leaf stage. Compared to wild-type (WT) plants, the sclerenchyma cells of bk5 stalks had a looser cell arrangement and thinner cell wall. Determination of cell wall composition showed that obvious differences in cellulose content, lignin content, starch content, and total soluble sugar were found between bk5 and WT stalks. Furthermore, we identified 226 differentially expressed genes (DEGs), with 164 genes significantly upregulated and 62 genes significantly downregulated in RNA-seq analysis. Some pathways related to cellulose and lignin synthesis, such as endocytosis and glycosylphosphatidylinositol (GPI)-anchored biosynthesis, were identified by the Kyoto Encyclopedia of Gene and Genomes (KEGG) and gene ontology (GO) analysis. In bulked-segregant sequence analysis (BSA-seq), we detected 2,931,692 high-quality Single Nucleotide Polymorphisms (SNPs) and identified five overlapped regions (11.2 Mb) containing 17 candidate genes with missense mutations or premature termination codons using the SNP-index methods. Some genes were involved in the cellulose synthesis-related genes such as ENTH/ANTH/VHS superfamily protein gene (endocytosis-related gene) and the lignin synthesis-related genes such as the cytochrome p450 gene. Some of these candidate genes identified from BSA-seq also existed with differential expression in RNA-seq analysis. These findings increase our understanding of the molecular mechanisms regulating the brittle stalk phenotype in maize.
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Affiliation(s)
- Jun Liu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Chuanbo Sun
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Siqi Guo
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiaohong Yin
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yuling Yuan
- Hulun Buir Agricultural Reclamation Technology Development Co., Ltd., Hailar, China
| | - Bing Fan
- Hulun Buir Agricultural Reclamation Technology Development Co., Ltd., Hailar, China
| | - Qingxue Lv
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Xinru Cai
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yi Zhong
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yuanfeng Xia
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Xiaomei Dong
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Zhifu Guo
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Guangshu Song
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Wei Huang
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
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7
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Liu H, Wang H, Shao C, Han Y, He Y, Yin Z. Genetic Architecture of Maize Stalk Diameter and Rind Penetrometer Resistance in a Recombinant Inbred Line Population. Genes (Basel) 2022; 13:genes13040579. [PMID: 35456384 PMCID: PMC9032882 DOI: 10.3390/genes13040579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Stalk lodging presents a major constraint on maize (Zea mays L.) quantity and quality and hampers mechanized grain harvesting. Stalk diameter (SD) and rind penetrometer resistance (RPR) are crucial indicators of stalk lodging. To dissect the genetic architecture of these indicators, we constructed a recombinant inbred line (RIL) population derived from a cross between maize inbred lines LDC-1 and YS501 to identify quantitative trait loci (QTLs) controlling SD and RPR. Corresponding phenotypes of basal second, third, and fourth internodes in four environments were determined. By integrating QTL mapping results based on individual environments and best linear unbiased prediction (BLUP) values, we identified 12, 12, and 13 QTLs associated with SD and 17, 14, and 17 associated with RPR. Each QTL accounted for 3.83–21.72% of phenotypic variation. For SD-related QTLs, 30 of 37 were enriched in 12 QTL clusters; similarly, RPR-related QTLs had 38 of 48 enriched in 12 QTL clusters. The stable QTL qSD9-2 for SD on chromosome 9 was validated and delimited within a physical region of 9.97 Mb. Confidence intervals of RPR-related QTLs contained 169 genes involved in lignin and polysaccharide biosynthesis, with 12 of these less than 500 kb from the peak of the corresponding QTL. Our results deepen our understanding of the genetic mechanism of maize stalk strength and provide a basis for breeding lodging resistance.
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Affiliation(s)
- Huanhuan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (H.L.); (H.W.); (C.S.); (Y.H.); (Y.H.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Huan Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (H.L.); (H.W.); (C.S.); (Y.H.); (Y.H.)
| | - Cong Shao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (H.L.); (H.W.); (C.S.); (Y.H.); (Y.H.)
| | - Youle Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (H.L.); (H.W.); (C.S.); (Y.H.); (Y.H.)
| | - Yonghui He
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (H.L.); (H.W.); (C.S.); (Y.H.); (Y.H.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhitong Yin
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (H.L.); (H.W.); (C.S.); (Y.H.); (Y.H.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Liu X, Hu X, Li K, Liu Z, Wu Y, Wang H, Huang C. Genetic mapping and genomic selection for maize stalk strength. BMC PLANT BIOLOGY 2020; 20:196. [PMID: 32380944 PMCID: PMC7204062 DOI: 10.1186/s12870-020-2270-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/29/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Maize is one of the most important staple crops and is widely grown throughout the world. Stalk lodging can cause enormous yield losses in maize production. However, rind penetrometer resistance (RPR), which is recognized as a reliable measurement to evaluate stalk strength, has been shown to be efficient and useful for improving stalk lodging-resistance. Linkage mapping is an acknowledged approach for exploring the genetic architecture of target traits. In addition, genomic selection (GS) using whole genome markers enhances selection efficiency for genetically complex traits. In the present study, two recombinant inbred line (RIL) populations were utilized to dissect the genetic basis of RPR, which was evaluated in seven growth stages. RESULTS The optimal stages to measure stalk strength are the silking phase and stages after silking. A total of 66 and 45 quantitative trait loci (QTL) were identified in each RIL population. Several potential candidate genes were predicted according to the maize gene annotation database and were closely associated with the biosynthesis of cell wall components. Moreover, analysis of gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway further indicated that genes related to cell wall formation were involved in the determination of RPR. In addition, a multivariate model of genomic selection efficiently improved the prediction accuracy relative to a univariate model and a model considering RPR-relevant loci as fixed effects. CONCLUSIONS The genetic architecture of RPR is highly genetically complex. Multiple minor effect QTL are jointly involved in controlling phenotypic variation in RPR. Several pleiotropic QTL identified in multiple stages may contain reliable genes and can be used to develop functional markers for improving the selection efficiency of stalk strength. The application of genomic selection to RPR may be a promising approach to accelerate breeding process for improving stalk strength and enhancing lodging-resistance.
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Affiliation(s)
- Xiaogang Liu
- Institute of Crop Sciences, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojiao Hu
- Institute of Crop Sciences, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kun Li
- Institute of Crop Sciences, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhifang Liu
- Institute of Crop Sciences, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yujin Wu
- Institute of Crop Sciences, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwu Wang
- Institute of Crop Sciences, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Changling Huang
- Institute of Crop Sciences, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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