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Li P, Zhang Z, Xiao G, Zhao Z, He K, Yang X, Pan Q, Mi G, Jia Z, Yan J, Chen F, Yuan L. Genomic basis determining root system architecture in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:102. [PMID: 38607439 DOI: 10.1007/s00122-024-04606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024]
Abstract
KEY MESSAGE A total of 389 and 344 QTLs were identified by GWAS and QTL mapping explaining accumulatively 32.2-65.0% and 23.7-63.4% of phenotypic variation for 14 shoot-borne root traits using more than 1300 individuals across multiple field trails. Efficient nutrient and water acquisition from soils depends on the root system architecture (RSA). However, the genetic determinants underlying RSA in maize remain largely unexplored. In this study, we conducted a comprehensive genetic analysis for 14 shoot-borne root traits using 513 inbred lines and 800 individuals from four recombinant inbred line (RIL) populations at the mature stage across multiple field trails. Our analysis revealed substantial phenotypic variation for these 14 root traits, with a total of 389 and 344 QTLs identified through genome-wide association analysis (GWAS) and linkage analysis, respectively. These QTLs collectively explained 32.2-65.0% and 23.7-63.4% of the trait variation within each population. Several a priori candidate genes involved in auxin and cytokinin signaling pathways, such as IAA26, ARF2, LBD37 and CKX3, were found to co-localize with these loci. In addition, a total of 69 transcription factors (TFs) from 27 TF families (MYB, NAC, bZIP, bHLH and WRKY) were found for shoot-borne root traits. A total of 19 genes including PIN3, LBD15, IAA32, IAA38 and ARR12 and 19 GWAS signals were overlapped with selective sweeps. Further, significant additive effects were found for root traits, and pyramiding the favorable alleles could enhance maize root development. These findings could contribute to understand the genetic basis of root development and evolution, and provided an important genetic resource for the genetic improvement of root traits in maize.
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Affiliation(s)
- Pengcheng Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zhihai Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Gui Xiao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Zheng Zhao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Kunhui He
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qingchun Pan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhongtao Jia
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fanjun Chen
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Lixing Yuan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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Kassem MA, Knizia D, Meksem K. A Summary of Two Decades of QTL and Candidate Genes That Control Seed Tocopherol Contents in Maize ( Zea mays L.). Genes (Basel) 2024; 15:472. [PMID: 38674406 PMCID: PMC11049817 DOI: 10.3390/genes15040472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Tocopherols are secondary metabolites synthesized through the shikimate biosynthetic pathway in the plastids of most plants. It is well known that α-Tocopherol (vitamin E) has many health benefits for humans and animals; therefore, it is highly used in human and animal diets. Tocopherols vary considerably in most crop (and plant) species and within cultivars of the same species depending on environmental and growth conditions; tocopherol content is a polygenic, complex traits, and its inheritance is poorly understood. The objective of this review paper was to summarize all identified quantitative trait loci (QTL) that control seed tocopherols and related contents identified in maize (Zea mays) during the past two decades (2002-2022). Candidate genes identified within these QTL regions are also discussed. The QTL described here, and candidate genes identified within these genomic regions could be used in breeding programs to develop maize cultivars with high, beneficial levels of seed tocopherol contents.
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Affiliation(s)
- My Abdelmajid Kassem
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
| | - Dounya Knizia
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (K.M.)
| | - Khalid Meksem
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (K.M.)
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3
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Gao J, Li J, Zhang J, Sun Y, Ju X, Li W, Duan H, Xue Z, Sun L, Hussain Sahito J, Fu Z, Zhang X, Tang J. Identification of Novel QTL for Mercury Accumulation in Maize Using an Enlarged SNP Panel. Genes (Basel) 2024; 15:257. [PMID: 38397246 PMCID: PMC10888321 DOI: 10.3390/genes15020257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, which has been reported in previous studies, is associated with the significant SNP chr6.S_155668107 in axis tissue. It encodes a cysteine proteinase inhibitor, implying its potential role in mitigating mercury toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation.
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Affiliation(s)
- Jionghao Gao
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jianxin Li
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jihong Zhang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Yan Sun
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Xiaolong Ju
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Wenlong Li
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Haiyang Duan
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Zhengjie Xue
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Li Sun
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Javed Hussain Sahito
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Zhiyuan Fu
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Xuehai Zhang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jihua Tang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
- The Shennong Laboratory, Zhengzhou 450002, China
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Somsri A, Chu SH, Nawade B, Lee CY, Park YJ. Harnessing γ-TMT Genetic Variations and Haplotypes for Vitamin E Diversity in the Korean Rice Collection. Antioxidants (Basel) 2024; 13:234. [PMID: 38397832 PMCID: PMC10886147 DOI: 10.3390/antiox13020234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Gamma-tocopherol methyltransferase (γ-TMT), a key gene in the vitamin E biosynthesis pathway, significantly influences the accumulation of tocochromanols, thereby determining rice nutritional quality. In our study, we analyzed the γ-TMT gene in 475 Korean rice accessions, uncovering 177 genetic variants, including 138 SNPs and 39 InDels. Notably, two functional SNPs, tmt-E2-28,895,665-G/A and tmt-E4-28,896,689-A/G, were identified, causing substitutions from valine to isoleucine and arginine to glycine, respectively, across 93 accessions. A positive Tajima's D value in the indica group suggests a signature of balancing selection. Haplotype analysis revealed 27 haplotypes, with two shared between cultivated and wild accessions, seven specific to cultivated accessions, and 18 unique to wild types. Further, profiling of vitamin E isomers in 240 accessions and their association with haplotypes revealed that Hap_2, distinguished by an SNP in the 3' UTR (tmt-3UTR-28,897,360-T/A) exhibited significantly lower α-tocopherol (AT), α-tocotrienol (AT3), total tocopherol, and total tocotrienol, but higher γ-tocopherol (GT) in the japonica group. Additionally, in the indica group, Hap_2 showed significantly higher AT, AT3, and total tocopherol, along with lower GT and γ-tocotrienol, compared to Hap_19, Hap_20, and Hap_21. Overall, this study highlights the genetic landscape of γ-TMT and provides a valuable genetic resource for haplotype-based breeding programs aimed at enhancing nutritional profiles.
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Affiliation(s)
- Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Sang-Ho Chu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Bhagwat Nawade
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
| | - Chang-Yong Lee
- Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan 31080, Republic of Korea;
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; (A.S.); (S.-H.C.); (B.N.)
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5
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Tibbs-Cortes LE, Guo T, Li X, Tanaka R, Vanous AE, Peters D, Gardner C, Magallanes-Lundback M, Deason NT, DellaPenna D, Gore MA, Yu J. Genomic prediction of tocochromanols in exotic-derived maize. THE PLANT GENOME 2023; 16:e20286. [PMID: 36575809 DOI: 10.1002/tpg2.20286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/16/2022] [Indexed: 06/17/2023]
Abstract
Tocochromanols (vitamin E) are an essential part of the human diet. Plant products, including maize (Zea mays L.) grain, are the major dietary source of tocochromanols; therefore, breeding maize with higher vitamin content (biofortification) could improve human nutrition. Incorporating exotic germplasm in maize breeding for trait improvement including biofortification is a promising approach and an important research topic. However, information about genomic prediction of exotic-derived lines using available training data from adapted germplasm is limited. In this study, genomic prediction was systematically investigated for nine tocochromanol traits within both an adapted (Ames Diversity Panel [AP]) and an exotic-derived (Backcrossed Germplasm Enhancement of Maize [BGEM]) maize population. Although prediction accuracies up to 0.79 were achieved using genomic best linear unbiased prediction (gBLUP) when predicting within each population, genomic prediction of BGEM based on an AP training set resulted in low prediction accuracies. Optimal training population (OTP) design methods fast and unique representative subset selection (FURS), maximization of connectedness and diversity (MaxCD), and partitioning around medoids (PAM) were adapted for inbreds and, along with the methods mean coefficient of determination (CDmean) and mean prediction error variance (PEVmean), often improved prediction accuracies compared with random training sets of the same size. When applied to the combined population, OTP designs enabled successful prediction of the rest of the exotic-derived population. Our findings highlight the importance of leveraging genotype data in training set design to efficiently incorporate new exotic germplasm into a plant breeding program.
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Affiliation(s)
| | - Tingting Guo
- Hubei Hongshan Laboratory, Wuhan, China
- Huazhong Agricultural Univ., Wuhan, China
| | - Xianran Li
- USDA ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA, USA
| | - Ryokei Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, USA
| | - Adam E Vanous
- USDA ARS, North Central Regional Plant Introduction Station, Ames, IA, USA
| | - David Peters
- USDA ARS, North Central Regional Plant Introduction Station, Ames, IA, USA
| | - Candice Gardner
- USDA ARS, North Central Regional Plant Introduction Station, Ames, IA, USA
| | | | - Nicholas T Deason
- Dep. of Biochemistry and Molecular Biology, Michigan State Univ., East Lansing, MI, USA
| | - Dean DellaPenna
- Dep. of Biochemistry and Molecular Biology, Michigan State Univ., East Lansing, MI, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, USA
| | - Jianming Yu
- Dep. of Agronomy, Iowa State Univ., Ames, IA, USA
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6
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Tanaka R, Wu D, Li X, Tibbs-Cortes LE, Wood JC, Magallanes-Lundback M, Bornowski N, Hamilton JP, Vaillancourt B, Li X, Deason NT, Schoenbaum GR, Buell CR, DellaPenna D, Yu J, Gore MA. Leveraging prior biological knowledge improves prediction of tocochromanols in maize grain. THE PLANT GENOME 2023; 16:e20276. [PMID: 36321716 DOI: 10.1002/tpg2.20276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
With an essential role in human health, tocochromanols are mostly obtained by consuming seed oils; however, the vitamin E content of the most abundant tocochromanols in maize (Zea mays L.) grain is low. Several large-effect genes with cis-acting variants affecting messenger RNA (mRNA) expression are mostly responsible for tocochromanol variation in maize grain, with other relevant associated quantitative trait loci (QTL) yet to be fully resolved. Leveraging existing genomic and transcriptomic information for maize inbreds could improve prediction when selecting for higher vitamin E content. Here, we first evaluated a multikernel genomic best linear unbiased prediction (MK-GBLUP) approach for modeling known QTL in the prediction of nine tocochromanol grain phenotypes (12-21 QTL per trait) within and between two panels of 1,462 and 242 maize inbred lines. On average, MK-GBLUP models improved predictive abilities by 7.0-13.6% when compared with GBLUP. In a second approach with a subset of 545 lines from the larger panel, the highest average improvement in predictive ability relative to GBLUP was achieved with a multi-trait GBLUP model (15.4%) that had a tocochromanol phenotype and transcript abundances in developing grain for a few large-effect candidate causal genes (1-3 genes per trait) as multiple response variables. Taken together, our study illustrates the enhancement of prediction models when informed by existing biological knowledge pertaining to QTL and candidate causal genes.
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Affiliation(s)
- Ryokei Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Di Wu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Xiaowei Li
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | | | - Joshua C Wood
- Institute for Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | | | - Nolan Bornowski
- Dep. of Plant Biology, Michigan State Univ., East Lansing, MI, 48824, USA
| | - John P Hamilton
- Institute for Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Brieanne Vaillancourt
- Institute for Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Xianran Li
- USDA ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA, 99164, USA
| | - Nicholas T Deason
- Dep. of Biochemistry and Molecular Biology, Michigan State Univ., East Lansing, MI, 48824, USA
| | | | - C Robin Buell
- Institute for Plant Breeding, Genetics & Genomics, Center for Applied Genetic Technologies, Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Dean DellaPenna
- Dep. of Biochemistry and Molecular Biology, Michigan State Univ., East Lansing, MI, 48824, USA
| | - Jianming Yu
- Dep. of Agronomy, Iowa State Univ., Ames, IA, 50011, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
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Hossain F, Jaiswal SK, Muthusamy V, Zunjare RU, Mishra SJ, Chand G, Bhatt V, Bhat JS, Das AK, Chauhan HS, Gupta HS. Enhancement of nutritional quality in maize kernel through marker-assisted breeding for vte4, crtRB1, and opaque2 genes. J Appl Genet 2023; 64:431-443. [PMID: 37450243 DOI: 10.1007/s13353-023-00768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 05/31/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Traditional maize is poor in vitamin-E [α-tocopherol (α-T): 6-8 ppm], vitamin-A [provitamin-A (proA): 1-2ppm], lysine (0.150-0.2-50%), and tryptophan (0.030-0.040%). Here, we combined favourable alleles of vte4, crtRB1, and opaque2 (o2) genes in the parents of maize hybrids, viz., APQH-10 (PMI-PV-9 × PMI-PV-14) and APQH-11 (PMI-PV-9 × PMI-PV-15) using molecular breeding. Gene-specific markers were successfully used to select vte4, crtRB1, and o2 in BC1F1, BC2F1, and BC2F2 generations. Simple sequence repeats (104-109) were used for background selection, leading to an average recovery of 94% recurrent parent genome. The introgressed inbreds possessed significantly higher α-T: 18.38 ppm, α-/γ-tocopherol (α-/γ-T: 52%), and α-/total tocopherol (α-/TT: 32%) compared to original inbreds (α-T: 8.17 ppm, α-/γ-T: 25%, α-/TT: 18%). These newly derived inbreds also possessed higher β-carotene (BC: 8.91 ppm), β-cryptoxanthin (BCX: 1.27 ppm), proA (9.54 ppm), lysine (0.348%), and tryptophan (0.082%) compared to traditional maize inbreds. The reconstituted hybrids recorded higher α-T (2.1-fold), α-/γ-T (1.9-fold), and α-/TT (1.6-fold) over the original hybrids. These reconstituted hybrids were also rich in BC (5.7-fold), BCX (3.3-fold), proA (5.3-fold), lysine (1.9-fold), and tryptophan (2.0-fold) over the traditional hybrids. The reconstituted hybrids had similar grain yield and phenotypic characteristics to original versions. These multinutrient-rich maize hybrids hold great potential to alleviate malnutrition in sustainable and cost-effective manner.
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Affiliation(s)
- Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Sunil K Jaiswal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vignesh Muthusamy
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajkumar U Zunjare
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Subhra J Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gulab Chand
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vinay Bhatt
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jayant S Bhat
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Abhijit K Das
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Hema S Chauhan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Hari S Gupta
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Liu Z, Li P, Ren W, Chen Z, Olukayode T, Mi G, Yuan L, Chen F, Pan Q. Hybrid performance evaluation and genome-wide association analysis of root system architecture in a maize association population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:194. [PMID: 37606710 DOI: 10.1007/s00122-023-04442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/04/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE The genetic architecture of RSA traits was dissected by GWAS and coexpression networks analysis in a maize association population. Root system architecture (RSA) is a crucial determinant of water and nutrient uptake efficiency in crops. However, the maize genetic architecture of RSA is still poorly understood due to the challenges in quantifying root traits and the lack of dense molecular markers. Here, an association mapping panel including 356 inbred lines were crossed with a common tester, Zheng58, and the test crosses were phenotyped for 12 RSA traits in three locations. We observed a 1.3 ~ sixfold phenotypic variation for measured RSA in the association panel. The association panel consisted of four subpopulations, non-stiff stalk (NSS) lines, stiff stalk (SS), tropical/subtropical (TST), and mixed. Zheng58 × TST has a 2.1% higher crown root number (CRN) and 8.6% less brace root number (BRN) than Zheng58 × NSS and Zheng58 × SS, respectively. Using a genome-wide association study (GWAS) with 1.25 million SNPs and correction for population structure, 191 significant SNPs were identified for root traits. Ninety (47%) of the significant SNPs showed positive allelic effects, and 101 (53%) showed negative effects. Each locus could explain 0.39% to 11.8% of phenotypic variation. By integrating GWAS results and comparing coexpression networks, 26 high-priority candidate genes were identified. Gene GRMZM2G377215, which belongs to the COBRA-like gene family, affected root growth and development. Gene GRMZM2G468657 encodes the aspartic proteinase nepenthesin-1, related to root development and N-deficient response. Collectively, our research provides progress in the genetic dissection of root system architecture. These findings present the further possibility for the genetic improvement of root traits in maize.
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Affiliation(s)
- Zhigang Liu
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Pengcheng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wei Ren
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Zhe Chen
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
| | - Toluwase Olukayode
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Guohua Mi
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Lixing Yuan
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
| | - Fanjun Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Qingchun Pan
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions of MOE, China Agricultural University, Beijing, China.
- Sanya Institute of China Agricultural University, Sanya, China.
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9
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Sethi M, Saini DK, Devi V, Kaur C, Singh MP, Singh J, Pruthi G, Kaur A, Singh A, Chaudhary DP. Unravelling the genetic framework associated with grain quality and yield-related traits in maize ( Zea mays L.). Front Genet 2023; 14:1248697. [PMID: 37609038 PMCID: PMC10440565 DOI: 10.3389/fgene.2023.1248697] [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: 06/27/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023] Open
Abstract
Maize serves as a crucial nutrient reservoir for a significant portion of the global population. However, to effectively address the growing world population's hidden hunger, it is essential to focus on two key aspects: biofortification of maize and improving its yield potential through advanced breeding techniques. Moreover, the coordination of multiple targets within a single breeding program poses a complex challenge. This study compiled mapping studies conducted over the past decade, identifying quantitative trait loci associated with grain quality and yield related traits in maize. Meta-QTL analysis of 2,974 QTLs for 169 component traits (associated with quality and yield related traits) revealed 68 MQTLs across different genetic backgrounds and environments. Most of these MQTLs were further validated using the data from genome-wide association studies (GWAS). Further, ten MQTLs, referred to as breeding-friendly MQTLs (BF-MQTLs), with a significant phenotypic variation explained over 10% and confidence interval less than 2 Mb, were shortlisted. BF-MQTLs were further used to identify potential candidate genes, including 59 genes encoding important proteins/products involved in essential metabolic pathways. Five BF-MQTLs associated with both quality and yield traits were also recommended to be utilized in future breeding programs. Synteny analysis with wheat and rice genomes revealed conserved regions across the genomes, indicating these hotspot regions as validated targets for developing biofortified, high-yielding maize varieties in future breeding programs. After validation, the identified candidate genes can also be utilized to effectively model the plant architecture and enhance desirable quality traits through various approaches such as marker-assisted breeding, genetic engineering, and genome editing.
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Affiliation(s)
- Mehak Sethi
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Veena Devi
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Charanjeet Kaur
- Department of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Mohini Prabha Singh
- Department of Floriculture and Landscaping, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jasneet Singh
- Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montreal, QC, Canada
| | - Gomsie Pruthi
- Department of Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amanpreet Kaur
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Alla Singh
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Dharam Paul Chaudhary
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
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10
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Lu J, Zhen S, Zhang J, Xie Y, He C, Wang X, Wang Z, Zhang S, Li Y, Cui Y, Wang G, Wang J, Liu J, Li L, Gu R, Zheng X, Fu J. Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:16. [PMID: 36662257 DOI: 10.1007/s00122-023-04293-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Long intergenic non-coding RNA (lincRNA), cis-acting expression quantitative trait locus (cis-eQTL), maize, regulatory evolution. The law of genetic variation during domestication explains the evolutionary mechanism and provides a theoretical basis for improving existing varieties of maize. Previous studies focused on exploiting regulatory variations controlling the expression of protein-coding genes rather than of non-protein-coding genes. Here, we examined the genetic and evolutionary features of long non-coding RNAs from intergenic regions (long intergenic non-coding RNAs, lincRNAs) using population-scale transcriptome data and identified 1168 lincRNAs with cis-acting expression quantitative trait loci (cis-eQTLs). We found that lincRNAs are more likely to be regulated by cis-eQTLs, which exert stronger effects than the protein-coding genes. During maize domestication and improvement, upregulated alleles of lincRNAs, which originated from both standing variation and new mutation, accumulate more frequently and show larger effect sizes than the coding genes. A stronger signature of genetic differentiation was observed in their regulatory regions compared to those of randomly sampled lincRNAs. In addition, we found that cis-regulatory differentiation of lincRNAs is related to the sequence conservation of lincRNA transcripts. Non-conserved lincRNAs more tend to gain upregulated alleles and show a stronger relationship with selected traits than conserved lincRNAs between maize and its wild relatives. Our findings in maize improve the understanding of cis-regulatory variation in lincRNA genes during domestication and improvement and provide an effective approach for prioritizing candidates for further investigation.
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Affiliation(s)
- Jiawen Lu
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sihan Zhen
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Zhang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuxin Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cheng He
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoli Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zheyuan Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Song Zhang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- 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
| | - Yu Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China
| | - Jianhua Wang
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Riliang Gu
- Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024, China.
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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11
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Devgan M, Gill GK, Praba UP, Singh G, Garg T, Karnatam KS, Kaur A, Vikal Y. Biochemical and molecular characterization of sub-tropical maize germplasm for tocopherols. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Jiang H, Shi Y, Liu J, Li Z, Fu D, Wu S, Li M, Yang Z, Shi Y, Lai J, Yang X, Gong Z, Hua J, Yang S. Natural polymorphism of ZmICE1 contributes to amino acid metabolism that impacts cold tolerance in maize. NATURE PLANTS 2022; 8:1176-1190. [PMID: 36241735 DOI: 10.1038/s41477-022-01254-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Cold stress negatively affects maize (Zea mays L.) growth, development and yield. Metabolic adjustments contribute to the adaptation of maize under cold stress. We show here that the transcription factor INDUCER OF CBF EXPRESSION 1 (ZmICE1) plays a prominent role in reprogramming amino acid metabolome and COLD-RESPONSIVE (COR) genes during cold stress in maize. Derivatives of amino acids glutamate/asparagine (Glu/Asn) induce a burst of mitochondrial reactive oxygen species, which suppress the cold-mediated induction of DEHYDRATION RESPONSE ELEMENT-BINDING PROTEIN 1 (ZmDREB1) genes and impair cold tolerance. ZmICE1 blocks this negative regulation of cold tolerance by directly repressing the expression of the key Glu/Asn biosynthesis genes, ASPARAGINE SYNTHETASEs. Moreover, ZmICE1 directly regulates the expression of DREB1s. Natural variation at the ZmICE1 promoter determines the binding affinity of the transcriptional activator ZmMYB39, a positive regulator of cold tolerance in maize, resulting in different degrees of ZmICE1 transcription and cold tolerance across inbred lines. This study thus unravels a mechanism of cold tolerance in maize and provides potential targets for engineering cold-tolerant varieties.
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Affiliation(s)
- Haifang Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jingyan Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- Fresh Corn Research Center of BTH, Tianjin Agricultural University, Tianjin, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Diyi Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Shifeng Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Minze Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Zijia Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Yunlu Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China.
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13
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Chauhan HS, Muthusamy V, Rashmi T, Basu S, Anand A, Mehta BK, Gain N, Zunjare RU, Singh AK, Gupta HS, Hossain F. Characterization of crtRB1- and vte4-based biofortified sweet corn inbreds for seed vigour and physico-biochemical traits. J Appl Genet 2022; 63:651-662. [PMID: 35972676 DOI: 10.1007/s13353-022-00715-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/18/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
Abstract
Sweet corn possessing recessive shrunken2 (sh2) gene is popular worldwide. Traditional sweet corn is poor in vitamin A and vitamin E. Plant breeders during the selection of sweet corn genotypes mainly emphasize on plant architecture and yield. Seed germination and seedling vigour play important role for early establishment in field, thereby increasing yield and income. Here, we analysed a set of 15 sh2-based biofortified sweet corn inbreds with crtRB1 (β-carotene hydroxylase1) and vte4 (γ-tocopherol methyltransferase) genes and three traditional sh2-based sweet corn inbreds for nutritional quality, seed vigour and various physico-biochemical traits. The newly developed inbreds possessed significantly higher provitamin A (proA: 15.60 µg/g) and vitamin E [α-tocopherol (α-T): 20.42 µg/g] than the traditional sweet corn inbreds (proA: 2.51 µg/g, α-T: 11.16 µg/g). The biofortified sweet corn inbreds showed wide variation for germination (80.67-87.33%), vigour index-I (2097.17-2925.28 cm), vigour index-II (134.27-216.19 mg) and electrical conductivity (10.19-13.21 μS cm-1 g-1). Wide variation was also observed for dehydrogenase (1.29-1.59 OD g-1 ml-1), super oxide dismutase (4.01-9.82 g-1), peroxidase (11.66-16.47 μM min-1 g-1), esterase (22.98-34.76 nM min-1 g-1) and α-amylase (5.91-8.15 OD g-1 ml-1). Enrichment of proA and vitamin E in sweet corn did not affect seed vigour and physico-biochemical traits. Correlation analysis revealed that electrical conductivity and α-amylase activity was the reliable indicator for assessing seed germination and vigour. The study identified superior biofortified sweet corn genotypes that would contribute to better vigour and establishment in field. This is the first report of analysis of biofortified sweet corn genotypes for seed vigour and physico-biochemical traits.
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Affiliation(s)
- Hema S Chauhan
- ICAR-Indian Agricultural Research Institute, New Delhi, India.,Amity Institute of Biotechnology, Amity University, Noida, India
| | | | - Tuhin Rashmi
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Sudipta Basu
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anjali Anand
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Brijesh K Mehta
- ICAR-Indian Agricultural Research Institute, New Delhi, India.,ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Nisrita Gain
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Ashok K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hari S Gupta
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, India.
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14
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Lv G, Chen X, Ying D, Li J, Fan Y, Wang B, Fang R. Marker-assisted pyramiding of γ-tocopherol methyltransferase and glutamate formiminotransferase genes for development of biofortified sweet corn hybrids. PeerJ 2022; 10:e13629. [PMID: 35818359 PMCID: PMC9270877 DOI: 10.7717/peerj.13629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/02/2022] [Indexed: 01/22/2023] Open
Abstract
Micronutrients, including vitamins, minerals, and other bioactive compounds, have tremendous impacts on human health. Much progress has been made in improving the micronutrient content of inbred lines in various crops through biofortified breeding. However, biofortified breeding still falls short for the rapid generation of high-yielding hybrids rich in multiple micronutrients. Here, we bred multi-biofortified sweet corn hybrids efficiently through marker-assisted selection. Screening by molecular markers for vitamin E and folic acid, we obtained 15 inbred lines carrying favorable alleles (six for vitamin E, nine for folic acid, and three for both). Multiple biofortified corn hybrids were developed through crossing and genetic diversity analysis.
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Affiliation(s)
- Guihua Lv
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang, China
| | - Xiaolong Chen
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang, China
| | - Duo Ying
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang, China
| | - Jiansheng Li
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Yinghu Fan
- Chuxiong Academy of Agricultural Sciences, Chuxiong, China
| | - Bin Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Ruiqiu Fang
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang, China
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15
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Wu D, Li X, Tanaka R, Wood JC, Tibbs-Cortes LE, Magallanes-Lundback M, Bornowski N, Hamilton JP, Vaillancourt B, Diepenbrock CH, Li X, Deason NT, Schoenbaum GR, Yu J, Buell CR, DellaPenna D, Gore MA. Combining GWAS and TWAS to identify candidate causal genes for tocochromanol levels in maize grain. Genetics 2022; 221:6603118. [PMID: 35666198 PMCID: PMC9339294 DOI: 10.1093/genetics/iyac091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/01/2022] [Indexed: 11/20/2022] Open
Abstract
Tocochromanols (tocopherols and tocotrienols, collectively vitamin E) are lipid-soluble antioxidants important for both plant fitness and human health. The main dietary sources of vitamin E are seed oils that often accumulate high levels of tocopherol isoforms with lower vitamin E activity. The tocochromanol biosynthetic pathway is conserved across plant species but an integrated view of the genes and mechanisms underlying natural variation of tocochromanol levels in seed of most cereal crops remains limited. To address this issue, we utilized the high mapping resolution of the maize Ames panel of ∼1,500 inbred lines scored with 12.2 million single-nucleotide polymorphisms to generate metabolomic (mature grain tocochromanols) and transcriptomic (developing grain) data sets for genetic mapping. By combining results from genome- and transcriptome-wide association studies, we identified a total of 13 candidate causal gene loci, including 5 that had not been previously associated with maize grain tocochromanols: 4 biosynthetic genes (arodeH2 paralog, dxs1, vte5, and vte7) and a plastid S-adenosyl methionine transporter (samt1). Expression quantitative trait locus (eQTL) mapping of these 13 gene loci revealed that they are predominantly regulated by cis-eQTL. Through a joint statistical analysis, we implicated cis-acting variants as responsible for colocalized eQTL and GWAS association signals. Our multiomics approach provided increased statistical power and mapping resolution to enable a detailed characterization of the genetic and regulatory architecture underlying tocochromanol accumulation in maize grain and provided insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in maize and other cereals.
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Affiliation(s)
| | | | | | - Joshua C Wood
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | | | - Maria Magallanes-Lundback
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Nolan Bornowski
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - John P Hamilton
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Brieanne Vaillancourt
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | | | - Xianran Li
- United States Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164, USA
| | - Nicholas T Deason
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - C Robin Buell
- Department of Crop & Soil Sciences, Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Dean DellaPenna
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Michael A Gore
- Corresponding author: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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16
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Hershberger J, Tanaka R, Wood JC, Kaczmar N, Wu D, Hamilton JP, DellaPenna D, Buell CR, Gore MA. Transcriptome-wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels. THE PLANT GENOME 2022; 15:e20197. [PMID: 35262278 DOI: 10.1002/tpg2.20197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Sweet corn (Zea mays L.) is consistently one of the most highly consumed vegetables in the United States, providing a valuable opportunity to increase nutrient intake through biofortification. Significant variation for carotenoid (provitamin A, lutein, zeaxanthin) and tocochromanol (vitamin E, antioxidants) levels is present in temperate sweet corn germplasm, yet previous genome-wide association studies (GWAS) of these traits have been limited by low statistical power and mapping resolution. Here, we employed a high-quality transcriptomic dataset collected from fresh sweet corn kernels to conduct transcriptome-wide association studies (TWAS) and transcriptome prediction studies for 39 carotenoid and tocochromanol traits. In agreement with previous GWAS findings, TWAS detected significant associations for four causal genes, β-carotene hydroxylase (crtRB1), lycopene epsilon cyclase (lcyE), γ-tocopherol methyltransferase (vte4), and homogentisate geranylgeranyltransferase (hggt1) on a transcriptome-wide level. Pathway-level analysis revealed additional associations for deoxy-xylulose synthase2 (dxs2), diphosphocytidyl methyl erythritol synthase2 (dmes2), cytidine methyl kinase1 (cmk1), and geranylgeranyl hydrogenase1 (ggh1), of which, dmes2, cmk1, and ggh1 have not previously been identified through maize association studies. Evaluation of prediction models incorporating genome-wide markers and transcriptome-wide abundances revealed a trait-dependent benefit to the inclusion of both genomic and transcriptomic data over solely genomic data, but both transcriptome- and genome-wide datasets outperformed a priori candidate gene-targeted prediction models for most traits. Altogether, this study represents an important step toward understanding the role of regulatory variation in the accumulation of vitamins in fresh sweet corn kernels.
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Affiliation(s)
- Jenna Hershberger
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Ryokei Tanaka
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Joshua C Wood
- Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Nicholas Kaczmar
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - Di Wu
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
| | - John P Hamilton
- Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Dean DellaPenna
- Dep. of Biochemistry and Molecular Biology, Michigan State Univ., East Lansing, MI, 48824, USA
| | - C Robin Buell
- Dep. of Crop & Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, 14853, USA
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17
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Qu Z, Wu Y, Hu D, Li T, Liang H, Ye F, Xue J, Xu S. Genome-Wide Association Analysis for Candidate Genes Contributing to Kernel-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:872292. [PMID: 35685022 PMCID: PMC9171146 DOI: 10.3389/fpls.2022.872292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/06/2022] [Indexed: 06/01/2023]
Abstract
Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize seed development and yield formation. In this study, two associated populations were used for genome-wide association analysis of kernel length, kernel width, kernel thickness, and hundred-kernel weight from multiple locations in AM122 and AM180, respectively. Then, genome-wide association mapping was performed based on the maize 6H90K SNP chip. A total of 139 loci were identified as associated with the four traits with p < 1 × 10-4 using two models (FarmCPU and MLM). The transcriptome data showed that 15 of them were expressed differentially in two maize-inbred lines KB182 (small kernel) and KB020 (big kernel) during kernel development. These candidate genes were enriched in regulating peroxidase activity, oxidoreductase, and leaf senescence. The molecular function was major in binding and catalytic activity. This study provided important reference information for exploring maize kernel development mechanisms and applying molecular markers in high-yield breeding.
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Affiliation(s)
- Zhibo Qu
- 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, China
- Maize Engineering Technology Research Centre, Yangling, 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, China
- Maize Engineering Technology Research Centre, Yangling, 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, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Ting Li
- 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, China
- Maize Engineering Technology Research Centre, Yangling, 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, China
- Maize Engineering Technology Research Centre, Yangling, 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, China
- Maize Engineering Technology Research Centre, Yangling, 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, China
- Maize Engineering Technology Research Centre, Yangling, 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, China
- Maize Engineering Technology Research Centre, Yangling, China
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18
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Liu M, Zhang M, Yu S, Li X, Zhang A, Cui Z, Dong X, Fan J, Zhang L, Li C, Ruan Y. A Genome-Wide Association Study Dissects the Genetic Architecture of the Metaxylem Vessel Number in Maize Brace Roots. FRONTIERS IN PLANT SCIENCE 2022; 13:847234. [PMID: 35360304 PMCID: PMC8961028 DOI: 10.3389/fpls.2022.847234] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 01/31/2022] [Indexed: 05/31/2023]
Abstract
Metaxylem vessels in maize brace roots are key tissue, and their number (MVN) affects plant water and inorganic salt transportation and lodging resistance. Dissecting the genetic basis of MVN in maize brace roots can help guide the genetic improvement of maize drought resistance and lodging resistance during late developmental stages. In this study, we used 508 inbred lines with tropical, subtropical, and temperate backgrounds to analyze the genetic architecture of MVN in maize brace roots. The phenotypic variation in MVN in brace roots was evaluated in three environments, which revealed broad natural variation and relative low levels of heritability (h 2 = 0.42). Stiff-stalk lines with a temperate background tended to have higher MVNs than plants in other genetic backgrounds. MVN was significantly positively correlated with plant height, tassel maximum axis length, ear length, and kernel number per row, which indicates that MVN may affect plant morphological development and yield. In addition, MVN was extremely significantly negatively correlated with brace root radius, but significantly positively correlated with brace root angle (BRA), diameter, and number, thus suggesting that the morphological function of some brace root traits may be essentially determined by MVN. Association analysis of MVN in brace roots combined 1,253,814 single nucleotide polymorphisms (SNPs) using FarmCPU revealed a total of nine SNPs significantly associated with MVN at P < 7.96 × 10-7. Five candidate genes for MVN that may participate in secondary wall formation (GRMZM2G168365, GRMZM2G470499, and GRMZM2G028982) and regulate flowering time (GRMZM2G381691 and GRMZM2G449165). These results provide useful information for understanding the genetic basis of MVN in brace root development. Further functional studies of identified candidate genes should help elucidate the molecular pathways that regulate MVN in maize brace roots.
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Affiliation(s)
- Meiling Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Meng Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiaoyang Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Zhenhai Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Jinjuan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Lijun Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
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19
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Xu G, Zhang X, Chen W, Zhang R, Li Z, Wen W, Warburton ML, Li J, Li H, Yang X. Population genomics of Zea species identifies selection signatures during maize domestication and adaptation. BMC PLANT BIOLOGY 2022; 22:72. [PMID: 35180846 PMCID: PMC8855575 DOI: 10.1186/s12870-022-03427-w] [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: 08/03/2021] [Accepted: 01/05/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND Maize (Zea mays L. ssp. mays) was domesticated from teosinte (Zea mays ssp. parviglumis) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide. Researchers have depicted the maize domestication and adaptation processes over the past two decades, but efforts have been limited either in sample size or genetic diversity. To better understand these processes, we conducted a genome-wide survey of 982 maize inbred lines and 190 teosinte accessions using over 40,000 single-nucleotide polymorphism markers. RESULTS Population structure, principal component analysis, and phylogenetic trees all confirmed the evolutionary relationship between maize and teosinte, and determined the evolutionary lineage of all species within teosinte. Shared haplotype analysis showed similar levels of ancestral alleles from Zea mays ssp. parviglumis and Zea mays ssp. mexicana in maize. Scans for selection signatures identified 394 domestication sweeps by comparing wild and cultivated maize and 360 adaptation sweeps by comparing tropical and temperate maize. Permutation tests revealed that the public association signals for flowering time were highly enriched in the domestication and adaptation sweeps. Genome-wide association study identified 125 loci significantly associated with flowering-time traits, ten of which identified candidate genes that have undergone selection during maize adaptation. CONCLUSIONS In this study, we characterized the history of maize domestication and adaptation at the population genomic level and identified hundreds of domestication and adaptation sweeps. This study extends the molecular mechanism of maize domestication and adaptation, and provides resources for basic research and genetic improvement in maize.
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Affiliation(s)
- Gen Xu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Wenkang Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Renyu Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhi Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Marilyn L Warburton
- United States of Department of Agriculture, Agricultural Research Service, Corn Host Plant Resistance Research Unit, Box 9555, Mississippi, MS, 39762, USA
| | - Jiansheng Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China.
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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20
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Chauhan HS, Chhabra R, Rashmi T, Muthusamy V, Zunjare RU, Mishra SJ, Gain N, Mehta BK, Singh AK, Gupta HS, Hossain F. Impact of vte4 and crtRB1 genes on composition of vitamin-E and provitamin-A carotenoids during kernel-stages in sweet corn. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104264] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Dou Y, Xia W, Mason AS, Huang D, Sun X, Fan H, Xiao Y. Developing functional markers for vitamin E biosynthesis in oil palm. PLoS One 2021; 16:e0259684. [PMID: 34797841 PMCID: PMC8604351 DOI: 10.1371/journal.pone.0259684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/24/2021] [Indexed: 11/19/2022] Open
Abstract
Vitamin E is essential for human health and plays positive roles in anti-oxidation. Previously, we detected large variation in vitamin E content among 161 oil palm accessions. In this study, twenty oil palm accessions with distinct variation in vitamin E contents (171.30 to 1 258.50 ppm) were selected for genetic variation analysis and developing functional markers associated with vitamin E contents. Thirty-seven homologous genes in oil palm belonging to vitamin E biosynthesis pathway were identified via BLASTP analysis, the lengths of which ranged from 426 to 25 717 bp (average 7 089 bp). Multiplex PCR sequencing for the 37 genes found 1 703 SNPs and 85 indels among the 20 oil palm accessions, with 226 SNPs locating in the coding regions. Clustering analysis for these polymorphic loci showed that the 20 oil palm accessions could be divided into five groups. Among these groups, group I included eight oil palm accessions whose vitamin E content (mean value: 893.50 ppm) was far higher than other groups (mean value 256.29 to 532.94 ppm). Correlation analysis between the markers and vitamin E traits showed that 134 SNP and 7 indel markers were significantly (p < 0.05) related with total vitamin E content. Among these functional markers, the indel EgTMT-1-24 was highly correlated with variation in vitamin E content, especially tocotrienol content. Our study identified a number of candidate function associated markers and provided clues for further research into molecular breeding for high vitamin E content oil palm.
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Affiliation(s)
- Yajing Dou
- College of Tropical Crops, Hainan University, Haikou, Hainan, P.R. China
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, Hainan, P.R. China
| | - Wei Xia
- College of Tropical Crops, Hainan University, Haikou, Hainan, P.R. China
| | - Annaliese S. Mason
- Plant Breeding Department, The University of Bonn, Bonn, North Rhine-Westphalia, Germany
| | - Dongyi Huang
- College of Tropical Crops, Hainan University, Haikou, Hainan, P.R. China
| | - Xiwei Sun
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, Hainan, P.R. China
| | - Haikuo Fan
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, Hainan, P.R. China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, Hainan, P.R. China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, P.R. China
- * E-mail: ,
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22
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Hu S, Wang M, Zhang X, Chen W, Song X, Fu X, Fang H, Xu J, Xiao Y, Li Y, Bai G, Li J, Yang X. Genetic basis of kernel starch content decoded in a maize multi-parent population. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2192-2205. [PMID: 34077617 PMCID: PMC8541773 DOI: 10.1111/pbi.13645] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 05/25/2023]
Abstract
Starch is the most abundant storage carbohydrate in maize kernels and provides calories for humans and other animals as well as raw materials for various industrial applications. Decoding the genetic basis of natural variation in kernel starch content is needed to manipulate starch quantity and quality via molecular breeding to meet future needs. Here, we identified 50 unique single quantitative trait loci (QTLs) for starch content with 18 novel QTLs via single linkage mapping, joint linkage mapping and a genome-wide association study in a multi-parent population containing six recombinant inbred line populations. Only five QTLs explained over 10% of phenotypic variation in single populations. In addition to a few large-effect and many small-effect additive QTLs, limited pairs of epistatic QTLs also contributed to the genetic basis of the variation in kernel starch content. A regional association study identified five non-starch-pathway genes that were the causal candidate genes underlying the identified QTLs for starch content. The pathway-driven analysis identified ZmTPS9, which encodes a trehalose-6-phosphate synthase in the trehalose pathway, as the causal gene for the QTL qSTA4-2, which was detected by all three statistical analyses. Knockout of ZmTPS9 increased kernel starch content and, in turn, kernel weight in maize, suggesting potential applications for ZmTPS9 in maize starch and yield improvement. These findings extend our knowledge about the genetic basis of starch content in maize kernels and provide valuable information for maize genetic improvement of starch quantity and quality.
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Affiliation(s)
- Shuting Hu
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Min Wang
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Xuan Zhang
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Wenkang Chen
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Xinran Song
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
- Agronomy CollegeXinjiang Agricultural UniversityUrumqiChina
| | - Xiuyi Fu
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
- Maize Research CenterBeijing Academy of Agriculture & Forestry Sciences (BAAFS)BeijingChina
| | - Hui Fang
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Jing Xu
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Yingni Xiao
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
- Crop Research InstituteGuangdong Academy of Agricultural SciencesKey Laboratory of Crops Genetics and Improvement of Guangdong ProvinceGuangzhouChina
| | - Yaru Li
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Guanghong Bai
- Agronomy CollegeXinjiang Agricultural UniversityUrumqiChina
| | - Jiansheng Li
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and BiochemistryNational Maize Improvement Center of ChinaMOA Key Lab of Maize BiologyChina Agricultural UniversityBeijingChina
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23
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Das AK, Gowda MM, Muthusamy V, Zunjare RU, Chauhan HS, Baveja A, Bhatt V, Chand G, Bhat JS, Guleria SK, Saha S, Gupta HS, Hossain F. Development of Maize Hybrids With Enhanced Vitamin-E, Vitamin-A, Lysine, and Tryptophan Through Molecular Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:659381. [PMID: 34367197 PMCID: PMC8335160 DOI: 10.3389/fpls.2021.659381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Malnutrition is a widespread problem that affects human health, society, and the economy. Traditional maize that serves as an important source of human nutrition is deficient in vitamin-E, vitamin-A, lysine, and tryptophan. Here, favorable alleles of vte4 (α-tocopherol methyl transferase), crtRB1 (β-carotene hydroxylase), lcyE (lycopene ε-cyclase), and o2 (opaque2) genes were combined in parental lines of four popular hybrids using marker-assisted selection (MAS). BC1F1, BC2F1, and BC2F2 populations were genotyped using gene-based markers of vte4, crtRB1, lcyE, and o2. Background selection using 81-103 simple sequence repeats (SSRs) markers led to the recovery of recurrent parent genome (RPG) up to 95.45%. Alpha (α)-tocopherol was significantly enhanced among introgressed progenies (16.13 μg/g) as compared to original inbreds (7.90 μg/g). Provitamin-A (proA) (10.42 μg/g), lysine (0.352%), and tryptophan (0.086%) were also high in the introgressed progenies. The reconstituted hybrids showed a 2-fold enhancement in α-tocopherol (16.83 μg/g) over original hybrids (8.06 μg/g). Improved hybrids also possessed high proA (11.48 μg/g), lysine (0.367%), and tryptophan (0.084%) when compared with traditional hybrids. The reconstituted hybrids recorded the mean grain yield of 8,066 kg/ha, which was at par with original hybrids (mean: 7,846 kg/ha). The MAS-derived genotypes resembled their corresponding original hybrids for the majority of agronomic and yield-related traits, besides characteristics related to distinctness, uniformity, and stability (DUS). This is the first report for the development of maize with enhanced vitamin-E, vitamin-A, lysine, and tryptophan.
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Affiliation(s)
- Abhijit K. Das
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Munegowda M. Gowda
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vignesh Muthusamy
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajkumar U. Zunjare
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hema S. Chauhan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Aanchal Baveja
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vinay Bhatt
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gulab Chand
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jayant S. Bhat
- Division of Genetics, IARI-Regional Research Centre, Dharwad, India
| | - Satish K. Guleria
- Plant Breeding, CSK Himachal Pradesh Krishi Vishvavidyalaya, Bajaura, India
| | - Supradip Saha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hari S. Gupta
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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24
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Medeiros DB, Brotman Y, Fernie AR. The utility of metabolomics as a tool to inform maize biology. PLANT COMMUNICATIONS 2021; 2:100187. [PMID: 34327322 PMCID: PMC8299083 DOI: 10.1016/j.xplc.2021.100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/26/2021] [Accepted: 04/19/2021] [Indexed: 05/04/2023]
Abstract
With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).
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Affiliation(s)
- David B. Medeiros
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
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25
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Genome-wide association studies: assessing trait characteristics in model and crop plants. Cell Mol Life Sci 2021; 78:5743-5754. [PMID: 34196733 PMCID: PMC8316211 DOI: 10.1007/s00018-021-03868-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/19/2023]
Abstract
GWAS involves testing genetic variants across the genomes of many individuals of a population to identify genotype–phenotype association. It was initially developed and has proven highly successful in human disease genetics. In plants genome-wide association studies (GWAS) initially focused on single feature polymorphism and recombination and linkage disequilibrium but has now been embraced by a plethora of different disciplines with several thousand studies being published in model and crop species within the last decade or so. Here we will provide a comprehensive review of these studies providing cases studies on biotic resistance, abiotic tolerance, yield associated traits, and metabolic composition. We also detail current strategies of candidate gene validation as well as the functional study of haplotypes. Furthermore, we provide a critical evaluation of the GWAS strategy and its alternatives as well as future perspectives that are emerging with the emergence of pan-genomic datasets.
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26
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Plant Transcription Factors Involved in Drought and Associated Stresses. Int J Mol Sci 2021; 22:ijms22115662. [PMID: 34073446 PMCID: PMC8199153 DOI: 10.3390/ijms22115662] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.
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27
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Shikha K, Shahi JP, Vinayan MT, Zaidi PH, Singh AK, Sinha B. Genome-wide association mapping in maize: status and prospects. 3 Biotech 2021; 11:244. [PMID: 33968587 PMCID: PMC8085158 DOI: 10.1007/s13205-021-02799-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association study (GWAS) provides a robust and potent tool to retrieve complex phenotypic traits back to their underlying genetics. Maize is an excellent crop for performing GWAS due to diverse genetic variability, rapid decay of linkage disequilibrium, availability of distinct sub-populations and abundant SNP information. The application of GWAS in maize has resulted in successful identification of thousands of genomic regions associated with many abiotic and biotic stresses. Many agronomic and quality traits of maize are severely affected by such stresses and, significantly affecting its growth and productivity. To improve productivity of maize crop in countries like India which contribute only 2% to the world's total production in 2019-2020, it is essential to understand genetic complexity of underlying traits. Various DNA markers and trait associations have been revealed using conventional linkage mapping methods. However, it has achieved limited success in improving polygenic complex traits due to lower resolution of trait mapping. The present review explores the prospects of GWAS in improving yield, quality and stress tolerance in maize besides, strengths and challenges of using GWAS for molecular breeding and genomic selection. The information gathered will facilitate elucidation of genetic mechanisms of complex traits and improve efficiency of marker-assisted selection in maize breeding. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02799-4.
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Affiliation(s)
- Kumari Shikha
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - J. P. Shahi
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - M. T. Vinayan
- International Maize and Wheat Improvement Centre (CIMMYT)-Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana India
| | - P. H. Zaidi
- International Maize and Wheat Improvement Centre (CIMMYT)-Asia, ICRISAT Campus, Patancheru, Hyderabad, Telangana India
| | - A. K. Singh
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
| | - B. Sinha
- Department of Genetics and Plant Breeding, Institute of Agriculltural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh India
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Gong D, Tan Z, Zhao H, Pan Z, Sun Q, Qiu F. Fine mapping of a kernel length-related gene with potential value for maize breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1033-1045. [PMID: 33459823 DOI: 10.1007/s00122-020-03749-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
A key candidate gene for maize kernel length was fine mapped to an interval of 942 kb; the locus significantly increases kernel length (KL) and hundred-kernel weight (HKW). Kernel size is a major determinant of yield in cereals. Kernel length, one of the determining factors of kernel size, is a target trait for both domestication and artificial breeding. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for kernel length in maize. In this project, a novel major QTL, named qKL9, controlling maize kernel length was identified. We verified the authenticity and stability of qKL9 via BC2F2 and BC3F1 populations, respectively, and ultimately mapped qKL9 to an ~ 942-kb genomic interval by testing the progenies of recombination events derived from BC3F2 and BC4F2 populations in multiple environments. Additionally, one new line (McqKL9-A) containing the ~ 942-kb segment was screened from the BC4F2 population. Combining transcriptome analysis between McqKL9-A and Mc at 6, 9 and 14 days after pollination and candidate regional association mapping, Zm00001d046723 was preliminarily identified as the key candidate gene for qKL9. Importantly, the replacement in the Mc line of the Mc's alleles by the V671's alleles in the qKL9 region improved the performances of single-cross hybrids obtained with elite lines, illustrating the potential value of this QTL for the genetic improvement in maize kernel-related traits. These findings facilitate molecular breeding for kernel size and cloning of the gene underlying qKL9, shedding light on the genetic basis of kernel size in maize.
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Affiliation(s)
- Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Zhenyuan Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, People's Republic of China.
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Jiang L, Strobbe S, Van Der Straeten D, Zhang C. Regulation of plant vitamin metabolism: backbone of biofortification for the alleviation of hidden hunger. MOLECULAR PLANT 2021; 14:40-60. [PMID: 33545049 DOI: 10.1016/j.molp.2020.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 05/04/2023]
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Yadav CB, Tokas J, Yadav D, Winters A, Singh RB, Yadav R, Gangashetty PI, Srivastava RK, Yadav RS. Identifying Anti-Oxidant Biosynthesis Genes in Pearl Millet [ Pennisetum glaucum (L.) R. Br.] Using Genome-Wide Association Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:599649. [PMID: 34122460 PMCID: PMC8194398 DOI: 10.3389/fpls.2021.599649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/19/2021] [Indexed: 05/05/2023]
Abstract
Pearl millet [Pennisetum glaucum (L.) R Br.] is an important staple food crop in the semi-arid tropics of Asia and Africa. It is a cereal grain that has the prospect to be used as a substitute for wheat flour for celiac patients. It is an important antioxidant food resource present with a wide range of phenolic compounds that are good sources of natural antioxidants. The present study aimed to identify the total antioxidant content of pearl millet flour and apply it to evaluate the antioxidant activity of its 222 genotypes drawn randomly from the pearl millet inbred germplasm association panel (PMiGAP), a world diversity panel of this crop. The total phenolic content (TPC) significantly correlated with DPPH (1,1-diphenyl-2-picrylhydrazyl) radical scavenging activity (% inhibition), which ranged from 2.32 to 112.45% and ferric-reducing antioxidant power (FRAP) activity ranging from 21.68 to 179.66 (mg ascorbic acid eq./100 g). Genome-wide association studies (GWAS) were conducted using 222 diverse accessions and 67 K SNPs distributed across all the seven pearl millet chromosomes. Approximately, 218 SNPs were found to be strongly associated with DPPH and FRAP activity at high confidence [-log (p) > 3.0-7.4]. Furthermore, flanking regions of significantly associated SNPs were explored for candidate gene harvesting. This identified 18 candidate genes related to antioxidant pathway genes (flavanone 7-O-beta-glycosyltransferase, GDSL esterase/lipase, glutathione S-transferase) residing within or near the association signal that can be selected for further functional characterization. Patterns of genetic variability and the associated genes reported in this study are useful findings, which would need further validation before their utilization in molecular breeding for high antioxidant-containing pearl millet cultivars.
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Affiliation(s)
- Chandra Bhan Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Jayanti Tokas
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Devvart Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Ana Winters
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Ram B. Singh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Rama Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | | | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Rattan S. Yadav
- Institute of Biological Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- *Correspondence: Rattan S. Yadav
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Assessment of the Potential for Genomic Selection To Improve Husk Traits in Maize. G3-GENES GENOMES GENETICS 2020; 10:3741-3749. [PMID: 32816916 PMCID: PMC7534435 DOI: 10.1534/g3.120.401600] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Husk has multiple functions such as protecting ears from diseases, infection, and dehydration during development. Additionally, husks comprised of fewer, shorter, thinner, and narrower layers allow faster moisture evaporation of kernels prior to harvest. Intensive studies have been conducted to identify appropriate husk architecture by understanding the genetic basis of related traits, including husk length, husk layer number, husk thickness, and husk width. However, marker-assisted selection is inefficient because the identified quantitative trait loci and associated genetic loci could only explain a small proportion of total phenotypic variation. Genomic selection (GS) has been used successfully on many species including maize on other traits. Thus, the potential of using GS for husk traits to directly identify superior inbred lines, without knowing the specific underlying genetic loci, is well worth exploring. In this study, we compared four GS models on a maize association population with 498 inbred lines belonging to four subpopulations, including 27 lines in stiff stalk, 67 lines in non-stiff stalk, 193 lines in tropical-subtropical, and 211 lines in mixture subpopulations. Genomic Best Linear Unbiased Prediction with principal components as cofactor, performed the best and was selected to examine the impact of interaction between sampling proportions and subpopulations. We found that predictions on inbred lines in a subpopulation were benefited from excluding individuals from other subpopulations for training if the training population within the subpopulation was large enough. Husk thickness exhibited the highest prediction accuracy among all husk traits. These results gave strategic insight to improve husk architecture.
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Guo J, Jin M, Chen Y, Liu J. An embedded gene selection method using knockoffs optimizing neural network. BMC Bioinformatics 2020; 21:414. [PMID: 32962627 PMCID: PMC7510330 DOI: 10.1186/s12859-020-03717-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/19/2020] [Indexed: 11/30/2022] Open
Abstract
Background Gene selection refers to find a small subset of discriminant genes from the gene expression profiles. How to select genes that affect specific phenotypic traits effectively is an important research work in the field of biology. The neural network has better fitting ability when dealing with nonlinear data, and it can capture features automatically and flexibly. In this work, we propose an embedded gene selection method using neural network. The important genes can be obtained by calculating the weight coefficient after the training is completed. In order to solve the problem of black box of neural network and further make the training results interpretable in neural network, we use the idea of knockoffs to construct the knockoff feature genes of the original feature genes. This method not only make each feature gene to compete with each other, but also make each feature gene compete with its knockoff feature gene. This approach can help to select the key genes that affect the decision-making of neural networks. Results We use maize carotenoids, tocopherol methyltransferase, raffinose family oligosaccharides and human breast cancer dataset to do verification and analysis. Conclusions The experiment results demonstrate that the knockoffs optimizing neural network method has better detection effect than the other existing algorithms, and specially for processing the nonlinear gene expression and phenotype data.
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Affiliation(s)
- Juncheng Guo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.,Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 10049, China.,School of Cyber Security, University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanyuan Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianxiao Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China. .,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Jiang S, Zhang H, Ni P, Yu S, Dong H, Zhang A, Cao H, Zhang L, Ruan Y, Cui Z. Genome-Wide Association Study Dissects the Genetic Architecture of Maize Husk Tightness. FRONTIERS IN PLANT SCIENCE 2020; 11:861. [PMID: 32695127 PMCID: PMC7338587 DOI: 10.3389/fpls.2020.00861] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/27/2020] [Indexed: 06/01/2023]
Abstract
The husk is a leafy outer tissue that encloses a maize ear. Previously, we identified the optimum husk structure by measuring the husk length, husk layer number, husk thickness and husk width. Husk tightness (HTI) is a combined trait based on the above four husk measurements. Unveiling the genetic basis of HTI will aid in guiding the genetic improvement of maize for mechanical harvesting and for protecting the ear from pest damage and pathogen infection. Here, we used a maize associate population of 508 inbred lines with tropical, subtropical and temperate backgrounds to analyze the genetic architecture of HTI. Evaluating the phenotypic diversity in three different environments showed that HTI exhibited broad natural variations and a moderate heritability level of 0.41. A diversity analysis indicated that the inbred lines having a temperate background were more loosely related than those having a tropical or subtropical background. HTI showed significant negative correlations with husk thickness and width, which indicates that thicker and wider husks wrapped the ear tighter than thinner and slimmer husks. Combining husk traits with ∼1.25 million single nucleotide polymorphisms in a genome-wide association study revealed 27 variants that were significantly associated with HTI above the threshold of P < 7.26 × 10-6. We found 27 candidate genes for HTI that may participate in (1) husk senescence involving lipid peroxidation (GRMZM2G017616) and programmed cell death (GRMZM2G168898 and GRMZM2G035045); (2) husk morphogenesis involving cell division (GRMZM5G869246) and cell wall architecture (GRMZM2G319798); and (3) cell signal transduction involving protein phosphorylation (GRMZM2G149277 and GRMZM2G004207) and the ABSISIC ACID INSENSITIVE3/VIVIPAROUS1 transcription factor (GRMZM2G088427). These results provide useful information for understanding the genetic basis of husk development. Further studies of identified candidate genes will help elucidate the molecular pathways that regulate HTI in maize.
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Affiliation(s)
- Siqi Jiang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Haibo Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Pengzun Ni
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Haixiao Dong
- College of Plant Sciences, Jilin University, Changchun, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Huiying Cao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Lijun Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
| | - Zhenhai Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, henyang, China
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang, China
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Denser Markers and Advanced Statistical Method Identified More Genetic Loci Associated with Husk Traits in Maize. Sci Rep 2020; 10:8165. [PMID: 32424146 PMCID: PMC7235265 DOI: 10.1038/s41598-020-65164-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/27/2020] [Indexed: 11/29/2022] Open
Abstract
The husk—the leaf-like outer covering of maize ear—has multiple functions, including protecting the ear from diseases infection and dehydration. In previous studies, we genotyped an association panel of 508 inbred lines genotyped with a total of ~550,000 SNPs (Illumina 50 K SNP Chip and RNA-seq). Genome-Wide Association Studies (GWAS) were conducted on four husk traits: husk length (HL), husk layer number (HN), husk thickness (HT), and husk width (HW). Minimal associations were identified and none of them passed the P-value threshold after a Bonferroni multiple-test correction using a single locus test in framework of mixed linear model. In this study, we doubled the number of SNPs (~1,250,000 in total) by adding GBS and 600 K SNP Chip. GWAS, performed with the recently developed multiple loci model (BLINK), revealed six genetic loci associated with HN and HT above the Bonferroni multiple-test threshold. Five candidate genes were identified based on the linkage disequilibrium with these loci, including GRMZM2G381691 and GRMZM2G012416. These two genes were up-regulation and down-regulation in all husk related tissues, respectively. GRMZM2G381691 associated with HT encoded a CCT domain protein, which expressed higher in tropical than temperate maize. GRMZM2G012416 associated with HN encoded an Armadillo (ARM) repeat protein, which regulated GA signal pathway. These associated SNPs and candidate genes paved a path to understand the genetic architecture of husk in maize.
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Palacios-Rojas N, McCulley L, Kaeppler M, Titcomb TJ, Gunaratna NS, Lopez-Ridaura S, Tanumihardjo SA. Mining maize diversity and improving its nutritional aspects within agro-food systems. Compr Rev Food Sci Food Saf 2020; 19:1809-1834. [PMID: 33337075 DOI: 10.1111/1541-4337.12552] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/05/2020] [Accepted: 02/09/2020] [Indexed: 12/16/2022]
Abstract
Agro-food systems are undergoing rapid innovation in the world and the system's continuum is promoted at different scales with one of the main outcomes to improve nutrition of consumers. Consumer knowledge through educational outreach is important to food and nutrition security and consumer demands guide breeding efforts. Maize is an important part of food systems. It is a staple food and together with rice and wheat, they provide 60% of the world's caloric intake. In addition to being a major contributor to global food and nutrition security, maize forms an important part of the culinary culture in many areas of Africa, the Americas, and Asia. Maize genetics are being exploited to improve human nutrition with the ultimate outcome of improving overall health. By impacting the health of maize consumers, market opportunities will be opened for maize producers with unique genotypes. Although maize is a great source of macronutrients, it is also a source of many micronutrients and phytochemicals purported to confer health benefits. The process of biofortification through traditional plant breeding has increased the protein, provitamin A carotenoid, and zinc contents of maize. The objective of this paper is to review the innovations developed and promoted to improve the nutritional profiles of maize and outcomes of the maize agro-food system.
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Affiliation(s)
| | - Laura McCulley
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin
| | - Mikayla Kaeppler
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin
| | - Tyler J Titcomb
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin
| | | | | | - Sherry A Tanumihardjo
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin
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Genetic variability for kernel tocopherols and haplotype analysis of γ-tocopherol methyl transferase (vte4) gene among exotic- and indigenous- maize inbreds. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Alves ML, Bento-Silva A, Carbas B, Gaspar D, Paulo M, Brites C, Mendes-Moreira P, Brites CM, Bronze MDR, Malosetti M, van Eeuwijk F, Vaz Patto MC. Alleles to Enhance Antioxidant Content in Maize-A Genome-Wide Association Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4051-4061. [PMID: 32141752 DOI: 10.1021/acs.jafc.9b07190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The interest in antioxidant compound breeding in maize (Zea mays L.), a major food crop, has increased in recent years. However, breeding of antioxidant compounds in maize can be hampered, given the complex genetic nature of these compounds. In this work, we followed a genome-wide association approach, using a unique germplasm collection (containing Portuguese germplasm), to study the genetic basis of several antioxidants in maize. Sixty-seven genomic regions associated with seven antioxidant compounds and two color-related traits were identified. Several significant associations were located within or near genes involved in the carotenoid (Zm00001d036345) and tocopherol biosynthetic pathways (Zm00001d017746). Some indications of a negative selection against α-tocopherol levels were detected in the Portuguese maize germplasm. The strongest single nucleotide polymorphism (SNP)-trait associations and the SNP alleles with larger effect sizes were pinpointed and set as priority for future validation studies; these associations detected now constitute a benchmark for developing molecular selection tools for antioxidant compound selection in maize.
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Affiliation(s)
- Mara Lisa Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Andreia Bento-Silva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Bruna Carbas
- Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Daniel Gaspar
- Instituto Politécnico de Coimbra, Escola Superior Agrária, Bencanta, 3045-601 Coimbra, Portugal
| | - Manuel Paulo
- Instituto Politécnico de Coimbra, Escola Superior Agrária, Bencanta, 3045-601 Coimbra, Portugal
| | - Cláudia Brites
- Instituto Politécnico de Coimbra, Escola Superior Agrária, Bencanta, 3045-601 Coimbra, Portugal
| | - Pedro Mendes-Moreira
- Instituto Politécnico de Coimbra, Escola Superior Agrária, Bencanta, 3045-601 Coimbra, Portugal
| | - Carla Moita Brites
- Instituto Nacional de Investigação Agrária e Veterinária, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Maria do Rosário Bronze
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Marcos Malosetti
- Biometris-Applied Statistics, Wageningen University, Radix, Building 107, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Fred van Eeuwijk
- Biometris-Applied Statistics, Wageningen University, Radix, Building 107, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
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Prasanna BM, Palacios-Rojas N, Hossain F, Muthusamy V, Menkir A, Dhliwayo T, Ndhlela T, San Vicente F, Nair SK, Vivek BS, Zhang X, Olsen M, Fan X. Molecular Breeding for Nutritionally Enriched Maize: Status and Prospects. Front Genet 2020; 10:1392. [PMID: 32153628 PMCID: PMC7046684 DOI: 10.3389/fgene.2019.01392] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Maize is a major source of food security and economic development in sub-Saharan Africa (SSA), Latin America, and the Caribbean, and is among the top three cereal crops in Asia. Yet, maize is deficient in certain essential amino acids, vitamins, and minerals. Biofortified maize cultivars enriched with essential minerals and vitamins could be particularly impactful in rural areas with limited access to diversified diet, dietary supplements, and fortified foods. Significant progress has been made in developing, testing, and deploying maize cultivars biofortified with quality protein maize (QPM), provitamin A, and kernel zinc. In this review, we outline the status and prospects of developing nutritionally enriched maize by successfully harnessing conventional and molecular marker-assisted breeding, highlighting the need for intensification of efforts to create greater impacts on malnutrition in maize-consuming populations, especially in the low- and middle-income countries. Molecular marker-assisted selection methods are particularly useful for improving nutritional traits since conventional breeding methods are relatively constrained by the cost and throughput of nutritional trait phenotyping.
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Affiliation(s)
| | | | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Vignesh Muthusamy
- ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Abebe Menkir
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | | | | | | | | | | | - Mike Olsen
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Xingming Fan
- Institute of Crop Sciences, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
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Jia H, Li M, Li W, Liu L, Jian Y, Yang Z, Shen X, Ning Q, Du Y, Zhao R, Jackson D, Yang X, Zhang Z. A serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield. Nat Commun 2020; 11:988. [PMID: 32080171 PMCID: PMC7033126 DOI: 10.1038/s41467-020-14746-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/30/2020] [Indexed: 11/09/2022] Open
Abstract
Increasing grain yield of maize (Zea mays L.) is required to meet the rapidly expanding demands for maize-derived food, feed, and fuel. Breeders have enhanced grain productivity of maize hybrids by pyramiding desirable characteristics for larger ears. However, loci selected for improving grain productivity remain largely unclear. Here, we show that a serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 (KNR6) determines pistillate floret number and ear length. Overexpression of KNR6 or introgression of alleles lacking the insertions of two transposable elements in the regulatory region of KNR6 can significantly enhance grain yield. Further in vitro evidences indicate that KNR6 can interact with an Arf GTPase-activating protein (AGAP) and its phosphorylation by KNR6 may affect ear length and kernel number. This finding provides knowledge basis to enhance maize hybrids grain yield.
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Affiliation(s)
- Haitao Jia
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Manfei Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Weiya Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Lab of Maize Biology, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, P. R. China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Yinan Jian
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zhixing Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Lab of Maize Biology, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, P. R. China
| | - Xiaomeng Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Qiang Ning
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Yanfang Du
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Ran Zhao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - David Jackson
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Lab of Maize Biology, Beijing Key Lab of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, P. R. China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
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40
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Luo T, Xia W, Gong S, Mason AS, Li Z, Liu R, Dou Y, Tang W, Fan H, Zhang C, Xiao Y. Identifying Vitamin E Biosynthesis Genes in Elaeis guineensis by Genome-Wide Association Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:678-685. [PMID: 31858793 DOI: 10.1021/acs.jafc.9b03832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Elaeis guineensis is a tropical oil crop and has the highest oil yield per unit area. Palm oil has high palmitic acid content and is also rich in vitamins, including vitamin E. We conducted genome-wide association studies in a diversity panel of 161 E. guineensis accessions to identify single-nucleotide polymorphisms (SNPs) linked with vitamin E and validated candidate genes in these marker-associated intervals. Based on the SNPs reported in our previous research, 47 SNP markers were detected to be significantly associated with the variation of tocopherol and tocotrienol content at a cutoff P value of 6.3 × 10-7. A total of 656 candidate genes in the flanking regions of the 47 SNPs were identified, followed by pathway enrichment analysis. Of these candidate genes, EgHGGT (homogentisate geranylgeranyl transferase) involved in the biosynthesis of tocotrienols had a higher expression level in the mesocarp compared to other tissues. Expression of the EgHGGT gene was positively correlated with the variation in α-tocotrienol content. Induced overexpression of the gene in Arabidopsis caused a significant increase in vitamin E content and production of α-tocotrienols compared to wild Arabidopsis.
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Affiliation(s)
- Tingting Luo
- National Research Center of Rapeseed Engineering and Technology, College of Plant Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Wei Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops , Hainan University , Haikou 570228 , P.R China
| | - Shufang Gong
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition , Justus Liebig University Giessen , Heinrich-Buff-Ring 26-32 , Giessen 35392i , Germany
| | - Zhiying Li
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
- Hainan Key Laboratory for Biosafe Monitoring and Molecular Breeding in Off-Season Reproduction Region , Institute of Tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , China
| | - Rui Liu
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Yajing Dou
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Wenqi Tang
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Haikuo Fan
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Chunyu Zhang
- National Research Center of Rapeseed Engineering and Technology, College of Plant Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Yong Xiao
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
- Hainan Key Laboratory for Biosafe Monitoring and Molecular Breeding in Off-Season Reproduction Region , Institute of Tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , China
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41
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Liu J, Fernie AR, Yan J. The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement. PLANT COMMUNICATIONS 2020; 1:100010. [PMID: 33404535 PMCID: PMC7747985 DOI: 10.1016/j.xplc.2019.100010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 05/14/2023]
Abstract
After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
| | - Alisdair R. Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
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Cao Y, Zhang M, Liang X, Li F, Shi Y, Yang X, Jiang C. Natural variation of an EF-hand Ca 2+-binding-protein coding gene confers saline-alkaline tolerance in maize. Nat Commun 2020; 11:186. [PMID: 31924762 PMCID: PMC6954252 DOI: 10.1038/s41467-019-14027-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 12/11/2019] [Indexed: 12/26/2022] Open
Abstract
Sodium (Na+) toxicity is one of the major damages imposed on crops by saline-alkaline stress. Here we show that natural maize inbred lines display substantial variations in shoot Na+ contents and saline-alkaline (NaHCO3) tolerance, and reveal that ZmNSA1 (Na+Content under Saline-Alkaline Condition) confers shoot Na+ variations under NaHCO3 condition by a genome-wide association study. Lacking of ZmNSA1 promotes shoot Na+ homeostasis by increasing root Na+ efflux. A naturally occurred 4-bp deletion decreases the translation efficiency of ZmNSA1 mRNA, thus promotes Na+ homeostasis. We further show that, under saline-alkaline condition, Ca2+ binds to the EF-hand domain of ZmNSA1 then triggers its degradation via 26S proteasome, which in turn increases the transcripts levels of PM-H+-ATPases (MHA2 and MHA4), and consequently enhances SOS1 Na+/H+ antiporter-mediated root Na+ efflux. Our studies reveal the mechanism of Ca2+-triggered saline-alkaline tolerance and provide an important gene target for breeding saline-alkaline tolerant maize varieties. Saline-alkaline stress affects worldwide crops production, but the tolerance mechanisms have not been fully elucidated. Here, the authors show that EF-hand Ca2 + -binding-protein coding gene ZmNSA1 can regulate root H + efflux, Na + homeostasis, and saline-alkaline tolerance in maize.
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Affiliation(s)
- Yibo Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Ming Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Xiaoyan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Fenrong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Yunlu Shi
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China.,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China.,Laboratory of Agrobiotechnology and National Maize Improvement Center of China, MOA Key Lab of Maize Biology, China Agricultural University, Beijing, 100193, China
| | - Caifu Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China. .,Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China. .,Outstanding Discipline Program for the Universities in Beijing, Beijing, 100094, China.
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43
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Park C, Dwiyanti MS, Nagano AJ, Liu B, Yamada T, Abe J. Identification of quantitative trait loci for increased α-tocopherol biosynthesis in wild soybean using a high-density genetic map. BMC PLANT BIOLOGY 2019; 19:510. [PMID: 31752696 PMCID: PMC6873731 DOI: 10.1186/s12870-019-2117-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/04/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Soybean is one of the most important crop sources of tocopherols (Toc). However, the content of α-Toc, an isoform with the highest vitamin E activity in humans, is low in most cultivars. With the aim of broadening genetic variability, we performed quantitative trait locus (QTL) analysis for a high seed α-Toc trait detected in a wild soybean and characterized the sequence polymorphisms and expression profiles of γ-tocopherol methyltransferase (γ-TMT) genes as potential candidates. RESULTS A recombinant inbred line population was developed from a cross between the low α-Toc breeding line TK780 and the high α-Toc wild accession B04009. The α-Toc content in seeds correlated strongly with the ratio of α-Toc to γ-Toc contents. QTL analysis using a high-density map constructed with 7710 single nucleotide polymorphisms (SNPs) generated by restriction site-associated DNA sequencing detected six QTLs involved in α-Toc biosynthesis. Of these, three in chromosomes (Chr) 9, 11, and 12 produced consistent effects during a 2-year trial. B04009 allele at QTLs in Chr9 and Chr12 and TK780 allele at the QTL in Chr11 each promoted the conversion of γ-Toc to α-Toc, which elevated the seed α-Toc content. SNPs and indels were detected between the parents in three γ-TMT genes (γ-TMT1, γ-TMT2, and γ-TMT3) co-located in the QTLs in Chr9 and Chr12, of which some existed in the cis-regulatory elements associated with seed development and functions. In immature cotyledons, γ-TMT3 was expressed at higher levels in B04009 than TK780, irrespective of two thermal conditions tested, whereas the expression of γ-TMT2 was markedly upregulated under higher temperatures, particularly in B04009. CONCLUSIONS We identified QTLs consistently controlling α-Toc biosynthesis in wild soybean seeds in 2-year trials. The QTL on Chr9 had been previously identified in soybean, whereas the QTLs on Chr11 and Chr12 were novel. Further molecular dissections and characterization of the QTLs may facilitate the use of high α-Toc alleles from wild soybean in soybean breeding and an understanding of the molecular mechanisms underlying α-Toc biosynthesis in soybean seeds.
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Affiliation(s)
- Cheolwoo Park
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | | | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, 520-2194, Japan
| | - Baohui Liu
- School of Life Science, Guangzhou University, Guangzhou, 510000, China
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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44
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Wang XQ, Kim KW, Chu SH, Phitaktansakul R, Park SW, Chung IM, Lee YS, Park YJ. Genome-Wide Association Study for Squalene Contents and Functional Haplotype Analysis in Rice. ACS OMEGA 2019; 4:19358-19365. [PMID: 31763560 PMCID: PMC6868895 DOI: 10.1021/acsomega.9b02754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
Squalene is an isoprenoid compound that acts as the intermediate metabolite in cholesterol synthesis. Squalene is not very susceptible to peroxidation, and it quenches singlet oxygen in the skin, which is caused by UV exposure and other ionizing radiation sources. Squalene is a precursor to phytosterol synthesis, and it has been widely studied for its ability to reduce oxidation, cancer activity, and cholesterol levels. We performed a genome-wide association study for squalene in rice using 1.6 million high-quality SNPs extracted from 295 accessions' resequencing data. The candidate gene locus Os09g0319800-an orthologue of terpene synthase in Arabidopsis-showed up as the most likely candidate gene amongst the identified loci. Nucleotide variations in the promoter were associated with squalene content variations within the japonica group. The results of this study can provide clues for understanding the mechanisms of squalene biosynthesis in rice.
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Affiliation(s)
- Xiao-Qiang Wang
- Department
of Plant Resources, College of Industrial Science and Center of Crop
Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic
of Korea
- DiaCarta
Inc. Yangzi Sci-Tech Innovation Center, Floor 21, Building A, No. 211 Pubin Road, Pukou District, Nanjing, Jiangsu 210000, China
| | - Kyu-Won Kim
- Department
of Plant Resources, College of Industrial Science and Center of Crop
Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic
of Korea
| | - Sang-Ho Chu
- Department
of Plant Resources, College of Industrial Science and Center of Crop
Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic
of Korea
| | - Rungnapa Phitaktansakul
- Department
of Plant Resources, College of Industrial Science and Center of Crop
Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic
of Korea
| | - Sang-Won Park
- Chemical
Safety Division, National Institute of Agriculture
Science (NIAS), Wanju 55365, Republic of Korea
| | - Ill-Min Chung
- Department
of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea
| | - Young-Sang Lee
- Department
of Medical Biotechnology, Soonchunhyang
University, Asan 31538, Republic of Korea
| | - Yong-Jin Park
- Department
of Plant Resources, College of Industrial Science and Center of Crop
Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic
of Korea
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45
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Wang QJ, Yuan Y, Liao Z, Jiang Y, Wang Q, Zhang L, Gao S, Wu F, Li M, Xie W, Liu T, Xu J, Liu Y, Feng X, Lu Y. Genome-Wide Association Study of 13 Traits in Maize Seedlings under Low Phosphorus Stress. THE PLANT GENOME 2019; 12:1-13. [PMID: 33016582 DOI: 10.3835/plantgenome2019.06.0039] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/06/2019] [Indexed: 06/11/2023]
Abstract
Low P stress is a global issue for grain production. Significant phenotypic differences were detected among 13 traits in 356 maize lines under P-sufficient and P-deficient conditions. Significant single nucleotide polymorphisms (SNPs) and low-P stress-responsive genes were identified for 13 maize root traits based on a genome-wide association study. Hap5, harboring 12 favorable SNPs, could enhance strong root systems and P absorption under low-P stress. Phosphorus is an essential macronutrient required for normal plant growth and development. Determining the genetic basis of root traits will enhance our understanding of maize's (Zea mays L.) tolerance to low-P stress. Here, we identified significant phenotypic differences for 13 traits in maize seedlings subjected to P-sufficient and P-deficient conditions. Six extremely sensitive and seven low-P stress tolerant inbreds were selected from 356 inbred lines of maize. No significant differences were observed between temperate and tropical-subtropical groups with respect to trait ratios associated with the adaptation to low-P stress. The broad-sense heritability of these traits ranged from relatively moderate (0.59) to high (0.90). Through genome-wide association mapping with 541,575 informative single nucleotide polymorphisms (SNPs), 551, 1140 and 1157 significant SNPs were detected for the 13 traits in 2012, 2016 and both years combined, respectively, along with 23 shared candidate genes, seven of which overlapped with reported quantitative trait loci and genes for low-P stress. Five haplotypes located in candidate gene GRMZM2G009544 were identified; among these, Hap5, harboring 12 favorable SNP alleles, showed significantly greater values for the root traits studied than the other four haplotypes under both experimental conditions. The candidate genes and favorable haplotypes and alleles identified here provide promising resources for genetic studies and molecular breeding for improving tolerance to abiotic stress in maize.
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Affiliation(s)
- Qing-Jun Wang
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Yibing Yuan
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Zhengqiao Liao
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Yi Jiang
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Litian Zhang
- College of Chuancha, Yibin Univ., Yibin, 644000, Sichuan, China
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Menglu Li
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Wubing Xie
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Tianhong Liu
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Yaxi Liu
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Xuanjun Feng
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
- State Key Lab. of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural Univ., Wenjiang, 611130, Sichuan, China
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Zhang L, Luo Y, Liu B, Zhang L, Zhang W, Chen R, Wang L. Overexpression of the maize γ-tocopherol methyltransferase gene (ZmTMT) increases α-tocopherol content in transgenic Arabidopsis and maize seeds. Transgenic Res 2019; 29:95-104. [PMID: 31673914 DOI: 10.1007/s11248-019-00180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/22/2019] [Indexed: 11/25/2022]
Abstract
The vitamin E family includes tocopherols and tocotrienols, which are essential lipid-soluble antioxidants necessary for human and livestock health. The seeds of many plant species, including maize, have high gamma (γ)-tocopherol but low alpha (α)-tocopherol contents; however, α-tocopherol is the most effective antioxidant. Therefore, it is necessary to optimize the tocopherol composition in plants. α-Tocopherol is synthesized from γ-tocopherol by γ-tocopherol methyltransferase (γ-TMT, VTE4) in the final step of the tocopherol biosynthetic pathway. In the present study, the full-length coding sequence (CDS) of γ-TMT was isolated from Zea mays, named ZmTMT. The ZmTMT CDS was 1059 bp in size, encoding 352 amino acids. Recombinant ZmTMT was expressed in Escherichia coli and the purified protein effectively converted γ-tocopherol into α-tocopherol in vitro. A comparison of enzyme activities showed that the activity of ZmTMT was higher than that of GmTMT2a (Glycine max) and AtTMT (Arabidopsis thaliana). Overexpression of ZmTMT increased the α-tocopherol content 4-5-fold in transgenic Arabidopsis and around 6.5-fold in transgenic maize kernels, and increased the α-/γ-tocopherol ratio to approximately 15 and 17, respectively. These results show that it is feasible to overexpress ZmTMT to optimize the tocopherol composition in maize; such a corn product might be useful in the feed industry in the near future.
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Affiliation(s)
- Lan Zhang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanzhong Luo
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bin Liu
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liang Zhang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Zhang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rumei Chen
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lei Wang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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47
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Zhan W, Liu J, Pan Q, Wang H, Yan S, Li K, Deng M, Li W, Liu N, Kong Q, Fernie AR, Yan J. An allele of ZmPORB2 encoding a protochlorophyllide oxidoreductase promotes tocopherol accumulation in both leaves and kernels of maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:114-127. [PMID: 31169939 DOI: 10.1111/tpj.14432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 05/15/2019] [Accepted: 05/20/2019] [Indexed: 05/27/2023]
Abstract
Phytol is one of the key precursors for tocopherol synthesis in plants, however, the underlying mechanisms concerning the accumulation of tocopherol remain poorly understood. In this study, qVE5, a major QTL affecting tocopherol accumulation in maize kernels was identified via a positional cloning approach. qVE5 encodes a protochlorophyllide oxidoreductase (ZmPORB2), which localizes to the chloroplast. Overexpression of ZmPORB2 increased tocopherol content in both leaves and kernels. Candidate gene association analysis identified a 5/8-bp insertion/deletion (InDel058) in the 5' untranslated region (UTR) as the causal polymorphism in affecting ZmPORB2 expression and being highly associated with tocopherol content. We showed that higher expression of ZmPORB2 correlated with more chlorophyll metabolites in the leaf following pollination. RNA-sequencing and metabolic analysis in near isogenic lines (NILs) support that ZmPORB2 participates in chlorophyll metabolism enabling the production of phytol, an important precursor of tocopherol. We also found that the tocopherol content in the kernel is mainly determined by the maternal genotype, a fact that was further confirmed by in vitro culture experiments. Finally, a PCR-based marker based on Indel058 was developed in order to facilitate the high tocopherol (vitamin E) maize breeding.
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Affiliation(s)
- Wei Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Crop Germplasm Resources of Northern China (Ministry of Education), Hebei Sub-center of National Maize Improvement Center of China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nannan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qian Kong
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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48
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Kimotho RN, Baillo EH, Zhang Z. Transcription factors involved in abiotic stress responses in Maize ( Zea mays L.) and their roles in enhanced productivity in the post genomics era. PeerJ 2019; 7:e7211. [PMID: 31328030 PMCID: PMC6622165 DOI: 10.7717/peerj.7211] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/26/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in various regions around the world, and recently, this has become a constant threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activities of transcription factors (TFs), which are families of genes coding for specific TF proteins. TF target genes form a regulon that is involved in the repression/activation of genes associated with abiotic stress responses. Therefore, it is of utmost importance to have a systematic study on each TF family, the downstream target genes they regulate, and the specific TF genes involved in multiple abiotic stress responses in maize and other staple crops. METHOD In this review, the main TF families, the specific TF genes and their regulons that are involved in abiotic stress regulation will be briefly discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from different plants like rice, Arabidopsis, wheat, and barley will be used. RESULTS We have described in detail the main TF families in maize that take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning, and RNA-Seq. CONCLUSION In conclusion, it is expected that all the information provided in this review will in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.
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Affiliation(s)
- Roy Njoroge Kimotho
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Elamin Hafiz Baillo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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49
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Pang J, Fu J, Zong N, Wang J, Song D, Zhang X, He C, Fang T, Zhang H, Fan Y, Wang G, Zhao J. Kernel size-related genes revealed by an integrated eQTL analysis during early maize kernel development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:19-32. [PMID: 30548709 PMCID: PMC6850110 DOI: 10.1111/tpj.14193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/05/2018] [Accepted: 11/16/2018] [Indexed: 05/21/2023]
Abstract
In maize, kernel traits strongly impact overall grain yields, and it is known that sophisticated spatiotemporal programs of gene expression coordinate kernel development, so advancing our knowledge of kernel development can help efforts to improve grain yields. Here, using phenotype, genotype and transcriptomics data of maize kernels at 5 and 15 days after pollination (DAP) for a large association mapping panel, we employed multiple quantitative genetics approaches-genome-wide association studies (GWAS) as well as expression quantitative trait loci (eQTL) and quantitative trait transcript (QTT) analyses-to gain insights about molecular genetic basis of kernel development in maize. This resulted in the identification of 137 putative kernel length-related genes at 5 DAP, of which 43 are located in previously reported QTL regions. Strikingly, we identified an eQTL that overlaps the locus encoding a maize homolog of the recently described m6 A methylation reader protein ECT2 from Arabidopsis; this putative epi eQTL is associated with 53 genes and may represent a master epi-transcriptomic regulator of kernel development. Notably, among the genes associated with this epi eQTL, 10 are for the main storage proteins in the maize endosperm (zeins) and two are known regulators of zein expression or endosperm development (Opaque2 and ZmICE1). Collectively, beyond cataloging and characterizing genomic attributes of a large number of eQTL associated with kernel development in maize, our study highlights how an eQTL approach can bolster the impact of both GWAS and QTT studies and can drive insights about the basic biology of plants.
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Affiliation(s)
- Junling Pang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Junjie Fu
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Na Zong
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Jing Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Dandan Song
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Xia Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Cheng He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Ting Fang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Hongwei Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Yunliu Fan
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
| | - Guoying Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing100081China
| | - Jun Zhao
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijing100081China
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50
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Baseggio M, Murray M, Magallanes-Lundback M, Kaczmar N, Chamness J, Buckler ES, Smith ME, DellaPenna D, Tracy WF, Gore MA. Genome-Wide Association and Genomic Prediction Models of Tocochromanols in Fresh Sweet Corn Kernels. THE PLANT GENOME 2019; 12:180038. [PMID: 30951088 DOI: 10.3835/plantgenome2018.06.0038] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Sweet corn ( L.), a highly consumed fresh vegetable in the United States, varies for tocochromanol (tocopherol and tocotrienol) levels but makes only a limited contribution to daily intake of vitamin E and antioxidants. We performed a genome-wide association study of six tocochromanol compounds and 14 derivative traits across a sweet corn inbred line association panel to identify genes associated with natural variation for tocochromanols and vitamin E in fresh kernels. Concordant with prior studies in mature maize kernels, an association was detected between γ-tocopherol methyltransferase (vte4) and α-tocopherol content, along with () and () for tocotrienol variation. Additionally, two kernel starch synthesis genes, () and (), were associated with tocotrienols, with the strongest evidence for in combination with fixed, strong and alleles, accounting for the greater amount of tocotrienols in and lines. In prediction models with genome-wide markers, predictive abilities were higher for tocotrienols than tocopherols, and these models were superior to those that used marker sets targeting a priori genes involved in the biosynthesis and/or genetic control of tocochromanols. Through this quantitative genetic analysis, we have established a key step for increasing tocochromanols in fresh kernels of sweet corn for human health and nutrition.
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