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Wang J, Zhao S, Zhang Y, Lu X, Du J, Wang C, Wen W, Guo X, Zhao C. Investigating the genetic basis of maize ear characteristics: a comprehensive genome-wide study utilizing high-throughput phenotypic measurement method and system. FRONTIERS IN PLANT SCIENCE 2023; 14:1248446. [PMID: 37701799 PMCID: PMC10493325 DOI: 10.3389/fpls.2023.1248446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023]
Abstract
The morphology of maize ears plays a critical role in the breeding of new varieties and increasing yield. However, the study of traditional ear-related traits alone can no longer meet the requirements of breeding. In this study, 20 ear-related traits, including size, shape, number, and color, were obtained in 407 maize inbred lines at two sites using a high-throughput phenotypic measurement method and system. Significant correlations were found among these traits, particularly the novel trait ear shape (ES), which was correlated with traditional traits: kernel number per row and kernel number per ear. Pairwise comparison tests revealed that the inbred lines of tropical-subtropical were significantly different from other subpopulations in row numbers per ear, kernel numbers per ear, and ear color. A genome-wide association study identified 275, 434, and 362 Single nucleotide polymorphisms (SNPs) for Beijing, Sanya, and best linear unbiased prediction scenarios, respectively, explaining 3.78% to 24.17% of the phenotypic variance. Furthermore, 58 candidate genes with detailed functional descriptions common to more than two scenarios were discovered, with 40 genes being associated with color traits on chromosome 1. After analysis of haplotypes, gene expression, and annotated information, several candidate genes with high reliability were identified, including Zm00001d051328 for ear perimeter and width, zma-MIR159f for ear shape, Zm00001d053080 for kernel width and row number per ear, and Zm00001d048373 for the blue color channel of maize kernels in the red-green-blue color model. This study emphasizes the importance of researching novel phenotypic traits in maize by utilizing high-throughput phenotypic measurements. The identified genetic loci enrich the existing genetic studies related to maize ears.
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Affiliation(s)
- Jinglu Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shuaihao Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ying Zhang
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xianju Lu
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chuanyu Wang
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Weiliang Wen
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xinyu Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunjiang Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Bhatt V, Muthusamy V, Panda KK, Katral A, Chhabra R, Mishra SJ, Gopinath I, Zunjare RU, Neeraja CN, Rakshit S, Yadava DK, Hossain F. Expression Dynamics of lpa1 Gene and Accumulation Pattern of Phytate in Maize Genotypes Possessing opaque2 and crtRB1 Genes at Different Stages of Kernel Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091745. [PMID: 37176803 PMCID: PMC10180721 DOI: 10.3390/plants12091745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Phytic acid (PA) acts as a storehouse for the majority of the mineral phosphorous (P) in maize; ~80% of the total P stored as phytate P is not available to monogastric animals and thereby causes eutrophication. In addition, phytic acid chelates positively charged minerals making them unavailable in the diet. The mutant lpa1-1 allele reduces PA more than the wild-type LPA1 allele. Further, mutant gene opaque2 (o2) enhances lysine and tryptophan and crtRB1 enhances provitamin-A (proA) more than wild-type O2 and CRTRB1 alleles, respectively. So far, the expression pattern of the mutant lpa1-1 allele has not been analysed in maize genotypes rich in lysine, tryptophan and proA. Here, we analysed the expression pattern of wild and mutant alleles of LPA1, O2 and CRTRB1 genes in inbreds with (i) mutant lpa1-1, o2 and crtRB1 alleles, (ii) wild-type LPA1 allele and mutant o2 and crtRB1 alleles and (iii) wild-type LPA1, O2 and CRTRB1 alleles at 15, 30 and 45 days after pollination (DAP). The average reduction of PA/total phosphorous (TP) in lpa1-1 mutant inbreds was 29.30% over wild-type LPA1 allele. The o2 and crtRB1-based inbreds possessed ~two-fold higher amounts of lysine and tryptophan, and four-fold higher amounts of proA compared to wild-type alleles. The transcript levels of lpa1-1, o2 and crtRB1 genes in lpa1-1-based inbreds were significantly lower than their wild-type versions across kernel development. The lpa1-1, o2 and crtRB1 genes reached their highest peak at 15 DAP. The correlation of transcript levels of lpa1-1 was positive for PA/TP (r = 0.980), whereas it was negative with inorganic phosphorous (iP) (r = -0.950). The o2 and crtRB1 transcripts showed negative correlations with lysine (r = -0.887) and tryptophan (r = -0.893), and proA (r = -0.940), respectively. This is the first comprehensive study on lpa1-1 expression in the maize inbreds during different kernel development stages. The information generated here offers great potential for comprehending the dynamics of phytic acid regulation in maize.
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Affiliation(s)
- Vinay Bhatt
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- AMITY Institute of Biotechnology, AMITY University, Noida 201313, Uttar Pradesh, India
| | - Vignesh Muthusamy
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Kusuma Kumari Panda
- AMITY Institute of Biotechnology, AMITY University, Noida 201313, Uttar Pradesh, India
| | - Ashvinkumar Katral
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rashmi Chhabra
- 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
| | - Ikkurti Gopinath
- 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
| | | | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, Ludhiana 141004, India
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India
| | - Devendra K Yadava
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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He L, Cheng L, Wang J, Liu J, Cheng J, Yang Z, Cao R, Han Y, Li H, Zhang B. Carotenoid Cleavage Dioxygenase 1 Catalyzes Lutein Degradation To Influence Carotenoid Accumulation and Color Development in Foxtail Millet Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9283-9294. [PMID: 35876162 DOI: 10.1021/acs.jafc.2c01951] [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] [Indexed: 06/15/2023]
Abstract
Foxtail millet is a minor but economically important crop in certain regions of the world. Millet color is often used to judge grain quality, yet the molecular determinants of millet coloration remain unclear. Here, we explored the relationship between SiCCD1 and millet coloration in yellow and white millet varieties. Carotenoid levels declined with grain maturation and were negatively correlated with SiCCD1 expression, which was significantly higher in white millet as compared to yellow millet during the color development stage. Cloning of the SiCCD1 promoter and CDS sequences from these different millet varieties revealed the presence of two additional cis-regulatory elements within the SiCCD1 promoter in white millet varieties, including an enhancer-like GC motif element associated with anoxic specific inducibility and a GCN4-motif element associated with endosperm expression. Dual-luciferase reporter assays confirmed that SiCCD1 promoter fragments containing these additional cis-acting elements derived from white millet varieties were significantly more active than those from yellow millet varieties, consistent with the observed SiCCD1 expression patterns. Further in vitro enzyme detection assays confirmed that SiCCD1 primarily targets and degrades lutein. Together, these data suggest that SiCCD1 promoter variation was a key factor associated with the observed differences in SiCCD1 expression, which in turn led to the difference in millet coloration.
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Affiliation(s)
- Lu He
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Maize Research Institute, Shanxi Agricultural University, Xinzhou 034000, China
| | - Lu Cheng
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Junjie Wang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Jing Liu
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Jinjin Cheng
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Zhirong Yang
- Department of Foundation, Shanxi Agricultural University, Taigu 030801, China
| | - Rui Cao
- Shanxi Biological Research Institute Co., Ltd, Taiyuan 030000, China
| | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu 030801, China
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China
| | - Hongying Li
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu 030801, China
| | - Bin Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu 030801, China
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-quality and Efficiency in Loess Plateau, Shanxi Agricultural University, Taigu 030801, China
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Baveja A, Chhabra R, Panda KK, Muthusamy V, Mehta BK, Mishra SJ, Zunjare RU, Hossain F. Expression analysis of opaque2, crtRB1 and shrunken2 genes during different stages of kernel development in biofortified sweet corn. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sun T, Rao S, Zhou X, Li L. Plant carotenoids: recent advances and future perspectives. MOLECULAR HORTICULTURE 2022; 2:3. [PMID: 37789426 PMCID: PMC10515021 DOI: 10.1186/s43897-022-00023-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/03/2022] [Indexed: 10/05/2023]
Abstract
Carotenoids are isoprenoid metabolites synthesized de novo in all photosynthetic organisms. Carotenoids are essential for plants with diverse functions in photosynthesis, photoprotection, pigmentation, phytohormone synthesis, and signaling. They are also critically important for humans as precursors of vitamin A synthesis and as dietary antioxidants. The vital roles of carotenoids to plants and humans have prompted significant progress toward our understanding of carotenoid metabolism and regulation. New regulators and novel roles of carotenoid metabolites are continuously revealed. This review focuses on current status of carotenoid metabolism and highlights recent advances in comprehension of the intrinsic and multi-dimensional regulation of carotenoid accumulation. We also discuss the functional evolution of carotenoids, the agricultural and horticultural application, and some key areas for future research.
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Affiliation(s)
- Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Sombir Rao
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Xuesong Zhou
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-Agricultural Research Service, Cornell University, Ithaca, NY, 14853, USA.
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
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AMORIM IS, ALMEIDA MCS, CHAVES RPF, CHISTÉ RC. Technological applications and color stability of carotenoids extracted from selected Amazonian fruits. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.01922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sun T, Zhu Q, Wei Z, Owens LA, Fish T, Kim H, Thannhauser TW, Cahoon EB, Li L. Multi-strategy engineering greatly enhances provitamin A carotenoid accumulation and stability in Arabidopsis seeds. ABIOTECH 2021; 2:191-214. [PMID: 36303886 PMCID: PMC9590580 DOI: 10.1007/s42994-021-00046-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/26/2021] [Indexed: 01/08/2023]
Abstract
Staple grains with low levels of provitamin A carotenoids contribute to the global prevalence of vitamin A deficiency and therefore are the main targets for provitamin A biofortification. However, carotenoid stability during both seed maturation and postharvest storage is a serious concern for the full benefits of carotenoid biofortified grains. In this study, we utilized Arabidopsis as a model to establish carotenoid biofortification strategies in seeds. We discovered that manipulation of carotenoid biosynthetic activity by seed-specific expression of Phytoene synthase (PSY) increases both provitamin A and total carotenoid levels but the increased carotenoids are prone to degradation during seed maturation and storage, consistent with previous studies of provitamin A biofortified grains. In contrast, stacking with Orange (OR His ), a gene that initiates chromoplast biogenesis, dramatically enhances provitamin A and total carotenoid content and stability. Up to 65- and 10-fold increases of β-carotene and total carotenoids, respectively, with provitamin A carotenoids composing over 63% were observed in the seeds containing OR His and PSY. Co-expression of Homogentisate geranylgeranyl transferase (HGGT) with OR His and PSY further increases carotenoid accumulation and stability during seed maturation and storage. Moreover, knocking-out of β-carotene hydroxylase 2 (BCH2) by CRISPR/Cas9 not only potentially facilitates β-carotene accumulation but also minimizes the negative effect of carotenoid over production on seed germination. Our findings provide new insights into various processes on carotenoid accumulation and stability in seeds and establish a multiplexed strategy to simultaneously target carotenoid biosynthesis, turnover, and stable storage for carotenoid biofortification in crop seeds. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00046-1.
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Affiliation(s)
- Tianhu Sun
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA.,Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Qinlong Zhu
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Ziqing Wei
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
| | - Lauren A Owens
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
| | - Tara Fish
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
| | - Hyojin Kim
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Theodore W Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA
| | - Edgar B Cahoon
- Department of Biochemistry and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853 USA.,Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
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