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Shi R, Cao Y, Yang T, Wang Y, Xiang Y, Chen F, Zhang W, Zhou X, Sun C, Fu S, Hu M, Zhang J, Wang X. Genome-Wide Association Study Reveals the Genetic Basis of Crude Fiber Components in Brassica napus L. Shoots at Stem Elongation Stage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16530-16540. [PMID: 39001851 DOI: 10.1021/acs.jafc.4c03032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Brassica napus is currently the principal field crop for producing materials for primary, secondary and tertiary industries. B. napus shoots at stem elongation stage are rich in anthocyanins, vitamin C and mineral elements such as selenium, calcium and zinc, and represent a new type of green vegetable. However, the high crude fiber (CF) content of B. napus shoots affects their taste, and few studies have focused on the quality traits of these vegetables. In this study, we investigated five traits related to the CF components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), hemicellulose (Hem) and cellulose (Cel), of B. napus shoots. Whole-genome resequencing at a depth of ∼20× was utilized to genotype an association panel of 202 diverse accessions, which resulted in the identification of 6,093,649 single nucleotide polymorphisms (SNPs) and 996,252 indels, respectively. A genome-wide association study (GWAS) was performed for the five CF-related traits based on the phenotypic data observed in four environments. A total of 1,285 significant SNPs were detected at the threshold of -log10 (p) = 5.16, and 97 significant association regions were obtained. In addition, seven candidate genes located on chromosomes A2 (one gene), A8 (three genes), A9 (two genes) and C9 (one gene) related to CF traits were identified, and ten lines containing low CF contents were selected as excellent germplasm resources for breeding. Our results contributed new insights into the genetic basis of CF traits and suggested germplasm resources for the quality improvement of B. napus shoots.
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Affiliation(s)
- Rui Shi
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, PR China
| | - Yu Cao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Tinghai Yang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Yaping Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Yanan Xiang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Feng Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Wei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Xiaoying Zhou
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Chengming Sun
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
| | - Sanxiong Fu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Maolong Hu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Jiefu Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Afairs, Nanjing 210014, PR China
- Yili Kazakh Autonmoous Prefecture Institure of Agricultural Science, Yining, Xinjiang 835000, PR China
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Daduwal HS, Bhardwaj R, Srivastava RK. Pearl millet a promising fodder crop for changing climate: a review. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:169. [PMID: 38913173 DOI: 10.1007/s00122-024-04671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/05/2024] [Indexed: 06/25/2024]
Abstract
The agricultural sector faces colossal challenges amid environmental changes and a burgeoning human population. In this context, crops must adapt to evolving climatic conditions while meeting increasing production demands. The dairy industry is anticipated to hold the highest value in the agriculture sector in future. The rise in the livestock population is expected to result in an increased demand for fodder feed. Consequently, it is crucial to seek alternative options, as crops demand fewer resources and are resilient to climate change. Pearl millet offers an apposite key to these bottlenecks, as it is a promising climate resilience crop with significantly low energy, water and carbon footprints compared to other crops. Numerous studies have explored its potential as a fodder crop, revealing promising performance. Despite its capabilities, pearl millet has often been overlooked. To date, few efforts have been made to document molecular aspects of fodder-related traits. However, several QTLs and candidate genes related to forage quality have been identified in other fodder crops, which can be harnessed to enhance the forage quality of pearl millet. Lately, excellent genomic resources have been developed in pearl millet allowing deployment of cutting-edge genomics-assisted breeding for achieving a higher rate of genetic gains. This review would facilitate a deeper understanding of various aspects of fodder pearl millet in retrospect along with the future challenges and their solution. This knowledge may pave the way for designing efficient breeding strategies in pearl millet thereby supporting sustainable agriculture and livestock production in a changing world.
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Affiliation(s)
- Harmanpreet Singh Daduwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Ruchika Bhardwaj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India.
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Karnatam KS, Mythri B, Un Nisa W, Sharma H, Meena TK, Rana P, Vikal Y, Gowda M, Dhillon BS, Sandhu S. Silage maize as a potent candidate for sustainable animal husbandry development-perspectives and strategies for genetic enhancement. Front Genet 2023; 14:1150132. [PMID: 37303948 PMCID: PMC10250641 DOI: 10.3389/fgene.2023.1150132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Maize is recognized as the queen of cereals, with an ability to adapt to diverse agroecologies (from 58oN to 55oS latitude) and the highest genetic yield potential among cereals. Under contemporary conditions of global climate change, C4 maize crops offer resilience and sustainability to ensure food, nutritional security, and farmer livelihood. In the northwestern plains of India, maize is an important alternative to paddy for crop diversification in the wake of depleting water resources, reduced farm diversity, nutrient mining, and environmental pollution due to paddy straw burning. Owing to its quick growth, high biomass, good palatability, and absence of anti-nutritional components, maize is also one of the most nutritious non-legume green fodders. It is a high-energy, low-protein forage commonly used for dairy animals like cows and buffalos, often in combination with a complementary high-protein forage such as alfalfa. Maize is also preferred for silage over other fodders due to its softness, high starch content, and sufficient soluble sugars required for proper ensiling. With a rapid population increase in developing countries like China and India, there is an upsurge in meat consumption and, hence, the requirement for animal feed, which entails high usage of maize. The global maize silage market is projected to grow at a compound annual growth rate of 7.84% from 2021 to 2030. Factors such as increasing demand for sustainable and environment-friendly food sources coupled with rising health awareness are fueling this growth. With the dairy sector growing at about 4%-5% and the increasing shortage faced for fodder, demand for silage maize is expected to increase worldwide. The progress in improved mechanization for the provision of silage maize, reduced labor demand, lack of moisture-related marketing issues as associated with grain maize, early vacancy of farms for next crops, and easy and economical form of feed to sustain household dairy sector make maize silage a profitable venture. However, sustaining the profitability of this enterprise requires the development of hybrids specific for silage production. Little attention has yet been paid to breeding for a plant ideotype for silage with specific consideration of traits such as dry matter yield, nutrient yield, energy in organic matter, genetic architecture of cell wall components determining their digestibility, stalk standability, maturity span, and losses during ensiling. This review explores the available information on the underlying genetic mechanisms and gene/gene families impacting silage yield and quality. The trade-offs between yield and nutritive value in relation to crop duration are also discussed. Based on available genetic information on inheritance and molecular aspects, breeding strategies are proposed to develop maize ideotypes for silage for the development of sustainable animal husbandry.
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Affiliation(s)
- Krishna Sai Karnatam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Bikkasani Mythri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Wajhat Un Nisa
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Heena Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Tarun Kumar Meena
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Prabhat Rana
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - M. Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Baldev Singh Dhillon
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Surinder Sandhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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Wan W, Wu Y, Hu D, Ye F, Wu X, Qi X, Liang H, Zhou H, Xue J, Xu S, Zhang X. Genome-wide association analysis of kernel nutritional quality in two natural maize populations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:18. [PMID: 37313300 PMCID: PMC10248675 DOI: 10.1007/s11032-023-01360-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/05/2023] [Indexed: 06/15/2023]
Abstract
As one of the three staple crops, nutritional traits in maize are important for human and animal nutrition. Grain quality-related traits are closely related to grain commercial value. Understanding the genetic basis of quality-related traits in maize would be helpful for breeding high-quality maize varieties. In this study, two association panels (AM122 and AM180) were subjected to genome-wide association analysis of grain quality-related traits, including protein content, oil content, starch content, and fiber content. In total, 98 SNPs (P < 1 × 10-4) were identified to be significantly associated with these four grain quality-related traits. By integrating two sets of public transcriptome data, 31 genes located in 200 kb regions flanking the associated SNP showed high expression during kernel development and were differentially expressed in two maize inbred lines, KA225 and KB035, with significantly different quality. These genes might regulate maize grain quality by participating in plant hormone processes, autophagy processes, and others. All these results could provide important reference information for breeding high‑quality maize varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01360-w.
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Affiliation(s)
- Wenting Wan
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Ying Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Die Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Fan Ye
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xiaopeng Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xingyue Qi
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Hangyu Liang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Haiyang Zhou
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
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Genetic Dissection and Germplasm Selection of the Low Crude Fiber Component in Brassica napus L. Shoots. Foods 2023; 12:foods12020403. [PMID: 36673495 PMCID: PMC9857593 DOI: 10.3390/foods12020403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Brassica napus is one of the most important oil crops in the world, and B. napus shoots are nutrient-rich fresh vegetables. The crude fiber (CF) component is one of the most important factors affecting the taste quality of B. napus shoots, but the factors underlying the desirable low-CF trait remain poorly understood. METHODS In this study, a high-density single-nucleotide polymorphism (SNP) map was used to map quantitative trait loci (QTLs) for five CF-related traits in a recombinant inbred population. RESULTS A total of 49 QTLs were obtained in four environments, including eleven, twelve, eight, twelve and six QTLs for content of neutral detergent fiber, acid detergent fiber, acid detergent lignin, hemicellulose and cellulose, respectively. The phenotypic variation explained by single QTL ranged from 4.62% to 14.76%. Eight of these QTLs were further integrated into four unique QTLs, which controlled two different traits simultaneously. Five CF-component-related candidate genes were identified, among which BnaC03g07110D and BnaC07g21271D were considered to be the most likely candidate genes. In addition, five lines with low CF content were selected, which can be used as excellent germplasm resources in breeding. CONCLUSIONS The QTLs identified in this study will contribute to our understanding of the genetic mechanism of CF and can be used as targets for reducing CF content in B. napus shoots. In addition, this study also provided excellent germplasm resources for low CF content breeding.
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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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Yang C, Zhang F, Jiang X, Yang X, He F, Wang Z, Long R, Chen L, Yang T, Wang C, Gao T, Kang J, Yang Q. Identification of Genetic Loci Associated With Crude Protein Content and Fiber Composition in Alfalfa ( Medicago sativa L.) Using QTL Mapping. FRONTIERS IN PLANT SCIENCE 2021; 12:608940. [PMID: 33679827 PMCID: PMC7933732 DOI: 10.3389/fpls.2021.608940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/27/2021] [Indexed: 05/17/2023]
Abstract
Forage quality determined mainly by protein content and fiber composition has a crucial influence on digestibility and nutrition intake for animal feeding. To explore the genetic basis of quality traits, we conducted QTL mapping based on the phenotypic data of crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), and lignin of an F1 alfalfa population generated by crossing of two alfalfa parents with significant difference in quality. In total, 83 QTLs were identified with contribution to the phenotypic variation (PVE) ranging from 1.45 to 14.35%. Among them, 47 QTLs interacted significantly with environment and 12 QTLs were associated with more than one trait. Epistatic effect was also detected for 73 pairs of QTLs with PVE of 1.08-14.06%. The results suggested that the inheritance of quality-related traits was jointly affected by additive, epistasis and environment. In addition, 83.33% of the co-localized QTLs were shared by ADF and NDF with the same genetic direction, while the additive effect of crude protein-associated QTLs was opposite to that fiber composition on the same locus, suggesting that the loci may antagonistically contribute to protein content and fiber composition. Further analysis of a QTL related to all the three traits of fiber composition (qNDF1C, qADF1C-2, and qlignin1C-2) showed that five candidate genes were homologs of cellulose synthase-like protein A1 in Medicago truncatula, indicating the potential role in fiber synthesis. For the protein-associated loci we identified, qCP4C-1 was located in the shortest region (chr 4.3 39.3-39.4 Mb), and two of the seven corresponding genes in this region were predicted to be E3 ubiquitin-protein ligase in protein metabolism. Therefore, our results provide some reliable regions significantly associated with alfalfa quality, and identification of the key genes would facilitate marker-assisted selection for favorable alleles in breeding program of alfalfa quality improvement.
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Affiliation(s)
- Changfu Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xijiang Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianhui Yang
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Chuan Wang
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Ting Gao
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Cuello C, Marchand P, Laurans F, Grand-Perret C, Lainé-Prade V, Pilate G, Déjardin A. ATR-FTIR Microspectroscopy Brings a Novel Insight Into the Study of Cell Wall Chemistry at the Cellular Level. FRONTIERS IN PLANT SCIENCE 2020; 11:105. [PMID: 32153612 PMCID: PMC7047332 DOI: 10.3389/fpls.2020.00105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/23/2020] [Indexed: 05/02/2023]
Abstract
Wood is a complex tissue that fulfills three major functions in trees: water conduction, mechanical support and nutrient storage. In Angiosperm trees, vessels, fibers and parenchyma rays are respectively assigned to these functions. Cell wall composition and structure strongly varies according to cell type, developmental stages and environmental conditions. This complexity can therefore hinder the study of the molecular mechanisms of wood formation, underlying the construction of its properties. However, this can be circumvented thanks to the development of cell-specific approaches and microphenotyping. Here, we present a non-destructive microphenotyping method based on attenuated total reflectance-Fourier transformed infrared (ATR-FTIR) microspectroscopy. We applied this technique to three types of poplar wood: normal wood of staked trees (NW), tension and opposite wood of artificially tilted trees (TW, OW). TW is produced by angiosperm trees in response to mechanical strains and is characterized by the presence of G fibers, exhibiting a thick gelatinous extra-layer, named G-layer, located in place of the usual S2 and/or S3 layers. By contrast, OW located on the opposite side of the trunk is totally deprived of fibers with G-layers. We developed a workflow for hyperspectral image analysis with both automatic pixel clustering according to cell wall types and identification of differentially absorbed wavenumbers (DAWNs). As pixel clustering failed to assign pixels to ray S-layers with sufficient efficiency, the IR profiling and identification of DAWNs were restricted to fiber and vessel cell walls. As reported elsewhere, this workflow identified cellulose as the main component of the G-layers, while the amount in acetylated xylans and lignins were shown to be reduced. These results validate ATR-FTIR technique for in situ characterization of G layers. In addition, this study brought new information about IR profiling of S-layers in TW, OW and NW. While OW and NW exhibited similar profiles, TW fibers S-layers combined characteristics of TW G-layers and of regular fiber S-layers. Unexpectedly, vessel S-layers of the three kinds of wood showed significant differences in IR profiling. In conclusion, ATR-FTIR microspectroscopy offers new possibilities for studying cell wall composition at the cell level.
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Affiliation(s)
| | | | - Françoise Laurans
- INRAE, ONF, BioForA, Orléans, France
- INRAE, Phenobois, Orléans, France
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Cuello C, Baldy A, Brunaud V, Joets J, Delannoy E, Jacquemot MP, Botran L, Griveau Y, Guichard C, Soubigou-Taconnat L, Martin-Magniette ML, Leroy P, Méchin V, Reymond M, Coursol S. A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PLoS One 2019; 14:e0227011. [PMID: 31891625 PMCID: PMC6938352 DOI: 10.1371/journal.pone.0227011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/09/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding the mechanisms triggering variation of cell wall degradability is a prerequisite to improving the energy value of lignocellulosic biomass for animal feed or biorefinery. Here, we implemented a multiscale systems approach to shed light on the genetic basis of cell wall degradability in maize. We demonstrated that allele replacement in two pairs of near-isogenic lines at a region encompassing a major quantitative trait locus (QTL) for cell wall degradability led to phenotypic variation of a similar magnitude and sign to that expected from a QTL analysis of cell wall degradability in the F271 × F288 recombinant inbred line progeny. Using DNA sequences within the QTL interval of both F271 and F288 inbred lines and Illumina RNA sequencing datasets from internodes of the selected near-isogenic lines, we annotated the genes present in the QTL interval and provided evidence that allelic variation at the introgressed QTL region gives rise to coordinated changes in gene expression. The identification of a gene co-expression network associated with cell wall-related trait variation revealed that the favorable F288 alleles exploit biological processes related to oxidation-reduction, regulation of hydrogen peroxide metabolism, protein folding and hormone responses. Nested in modules of co-expressed genes, potential new cell-wall regulators were identified, including two transcription factors of the group VII ethylene response factor family, that could be exploited to fine-tune cell wall degradability. Overall, these findings provide new insights into the regulatory mechanisms by which a major locus influences cell wall degradability, paving the way for its map-based cloning in maize.
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Affiliation(s)
- Clément Cuello
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Aurélie Baldy
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Johann Joets
- Génétique Quantitative et Evolution—Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Marie-Pierre Jacquemot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Lucy Botran
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Yves Griveau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Cécile Guichard
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Gif-sur-Yvette, France
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Université Paris-Diderot, Sorbonne Paris-Cité, Gif-sur-Yvette, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | | | - Valérie Méchin
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Matthieu Reymond
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Sylvie Coursol
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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Mahender A, Swamy BPM, Anandan A, Ali J. Tolerance of Iron-Deficient and -Toxic Soil Conditions in Rice. PLANTS (BASEL, SWITZERLAND) 2019; 8:E31. [PMID: 30696039 PMCID: PMC6409647 DOI: 10.3390/plants8020031] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/04/2023]
Abstract
Iron (Fe) deficiency and toxicity are the most widely prevalent soil-related micronutrient disorders in rice (Oryza sativa L.). Progress in rice cultivars with improved tolerance has been hampered by a poor understanding of Fe availability in the soil, the transportation mechanism, and associated genetic factors for the tolerance of Fe toxicity soil (FTS) or Fe deficiency soil (FDS) conditions. In the past, through conventional breeding approaches, rice varieties were developed especially suitable for low- and high-pH soils, which indirectly helped the varieties to tolerate FTS and FDS conditions. Rice-Fe interactions in the external environment of soil, internal homeostasis, and transportation have been studied extensively in the past few decades. However, the molecular and physiological mechanisms of Fe uptake and transport need to be characterized in response to the tolerance of morpho-physiological traits under Fe-toxic and -deficient soil conditions, and these traits need to be well integrated into breeding programs. A deeper understanding of the several factors that influence Fe absorption, uptake, and transport from soil to root and above-ground organs under FDS and FTS is needed to develop tolerant rice cultivars with improved grain yield. Therefore, the objective of this review paper is to congregate the different phenotypic screening methodologies for prospecting tolerant rice varieties and their responsible genetic traits, and Fe homeostasis related to all the known quantitative trait loci (QTLs), genes, and transporters, which could offer enormous information to rice breeders and biotechnologists to develop rice cultivars tolerant of Fe toxicity or deficiency. The mechanism of Fe regulation and transport from soil to grain needs to be understood in a systematic manner along with the cascade of metabolomics steps that are involved in the development of rice varieties tolerant of FTS and FDS. Therefore, the integration of breeding with advanced genome sequencing and omics technologies allows for the fine-tuning of tolerant genotypes on the basis of molecular genetics, and the further identification of novel genes and transporters that are related to Fe regulation from FTS and FDS conditions is incredibly important to achieve further success in this aspect.
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Affiliation(s)
- Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - B P Mallikarjuna Swamy
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
| | - Annamalai Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha 753006, India.
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines.
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Turner SD, Ellison SL, Senalik DA, Simon PW, Spalding EP, Miller ND. An Automated Image Analysis Pipeline Enables Genetic Studies of Shoot and Root Morphology in Carrot ( Daucus carota L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1703. [PMID: 30542356 PMCID: PMC6277879 DOI: 10.3389/fpls.2018.01703] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/01/2018] [Indexed: 05/04/2023]
Abstract
Carrot is a globally important crop, yet efficient and accurate methods for quantifying its most important agronomic traits are lacking. To address this problem, we developed an automated image analysis platform that extracts components of size and shape for carrot shoots and roots, which are necessary to advance carrot breeding and genetics. This method reliably measured variation in shoot size and shape, petiole number, petiole length, and petiole width as evidenced by high correlations with hundreds of manual measurements. Similarly, root length and biomass were accurately measured from the images. This platform also quantified shoot and root shapes in terms of principal components, which do not have traditional, manually measurable equivalents. We applied the pipeline in a study of a six-parent diallel population and an F2 mapping population consisting of 316 individuals. We found high levels of repeatability within a growing environment, with low to moderate repeatability across environments. We also observed co-localization of quantitative trait loci for shoot and root characteristics on chromosomes 1, 2, and 7, suggesting these traits are controlled by genetic linkage and/or pleiotropy. By increasing the number of individuals and phenotypes that can be reliably quantified, the development of a rapid, automated image analysis pipeline to measure carrot shoot and root morphology will expand the scope and scale of breeding and genetic studies.
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Affiliation(s)
- Sarah D. Turner
- Department of Horticulture, University of Wisconsin–Madison, Madison, WI, United States
| | - Shelby L. Ellison
- Vegetable Crops Research Unit, United States Department of Agriculture–Agricultural Research Service, Madison, WI, United States
| | - Douglas A. Senalik
- Vegetable Crops Research Unit, United States Department of Agriculture–Agricultural Research Service, Madison, WI, United States
| | - Philipp W. Simon
- Department of Horticulture, University of Wisconsin–Madison, Madison, WI, United States
- Vegetable Crops Research Unit, United States Department of Agriculture–Agricultural Research Service, Madison, WI, United States
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Nathan D. Miller
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
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Ma L, Liu M, Yan Y, Qing C, Zhang X, Zhang Y, Long Y, Wang L, Pan L, Zou C, Li Z, Wang Y, Peng H, Pan G, Jiang Z, Shen Y. Genetic Dissection of Maize Embryonic Callus Regenerative Capacity Using Multi-Locus Genome-Wide Association Studies. FRONTIERS IN PLANT SCIENCE 2018; 9:561. [PMID: 29755499 PMCID: PMC5933171 DOI: 10.3389/fpls.2018.00561] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/10/2018] [Indexed: 05/04/2023]
Abstract
The regenerative capacity of the embryonic callus, a complex quantitative trait, is one of the main limiting factors for maize transformation. This trait was decomposed into five traits, namely, green callus rate (GCR), callus differentiating rate (CDR), callus plantlet number (CPN), callus rooting rate (CRR), and callus browning rate (CBR). To dissect the genetic foundation of maize transformation, in this study multi-locus genome-wide association studies (GWAS) for the five traits were performed in a population of 144 inbred lines genotyped with 43,427 SNPs. Using the phenotypic values in three environments and best linear unbiased prediction (BLUP) values, as a result, a total of 127, 56, 160, and 130 significant quantitative trait nucleotides (QTNs) were identified by mrMLM, FASTmrEMMA, ISIS EM-BLASSO, and pLARmEB, respectively. Of these QTNs, 63 QTNs were commonly detected, including 15 across multiple environments and 58 across multiple methods. Allele distribution analysis showed that the proportion of superior alleles for 36 QTNs was <50% in 31 elite inbred lines. Meanwhile, these superior alleles had obviously additive effect on the regenerative capacity. This indicates that the regenerative capacity-related traits can be improved by proper integration of the superior alleles using marker-assisted selection. Moreover, a total of 40 candidate genes were found based on these common QTNs. Some annotated genes were previously reported to relate with auxin transport, cell fate, seed germination, or embryo development, especially, GRMZM2G108933 (WOX2) was found to promote maize transgenic embryonic callus regeneration. These identified candidate genes will contribute to a further understanding of the genetic foundation of maize embryonic callus regeneration.
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Affiliation(s)
- Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Min Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanyuan Yan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chunyan Qing
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yun Long
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lei Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhaoling Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanli Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huanwei Peng
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhou Jiang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yaou Shen
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