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Liao S, Zhang Y, Wang J, Zhao C, Ruan YL, Guo X. Exploring the Developmental Progression of Endosperm Cavity Formation in Maize Grain and the Underlying Molecular Basis Using X-Ray Tomography and Genome Wide Association Study. FRONTIERS IN PLANT SCIENCE 2022; 13:847884. [PMID: 35463403 PMCID: PMC9021861 DOI: 10.3389/fpls.2022.847884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Endosperm cavity (EC) in maize grain reduces yield and causes grain breakage during mechanical harvesting, hence representing a major problem in the maize industry. Despite this, little is known regarding the biological processes governing EC formation. Here, we attempted to address this issue by (i) determining the spatial and temporal progression of EC in a non-invasive manner and (ii) identifying candidate genes that may be linked to the formation of EC by using a genome wide association study (GWAS). Visualization and measurement using X-ray micro-computed tomography established that EC first appeared at the central starch endosperm at about 12 days after pollination (DAP) and became enlarged thereafter. GWAS-based screening of a panel of 299 inbred lines with a wide range of EC size identified nine candidate genes that showed significant association with EC formation. Most of the candidate genes exhibited a decrease at 12 DAP, coinciding with the timing of EC appearance. Among them, ZmMrp11 was annotated as a member encoding a multidrug resistance-associated protein that has been shown in other studies to sequestrate toxic metabolites from the cytosol to the vacuole, thereby detoxifying the cellular environment. This, together with the reduced expression of ZmMrp11 in maize grains from 12 DAP, prompted us to propose that the low expression of ZmMrp11 may block cellular detoxification in the maize endosperm cells, leading to cell death and ultimately the formation of EC.
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Affiliation(s)
- Shengjin Liao
- Beijing Key Laboratory of Digital Plant, Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Ying Zhang
- Beijing Key Laboratory of Digital Plant, Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinglu Wang
- Beijing Key Laboratory of Digital Plant, Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunjiang Zhao
- Beijing Key Laboratory of Digital Plant, Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yong-Ling Ruan
- Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Xinyu Guo
- Beijing Key Laboratory of Digital Plant, Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Sharma SP, Zuo T, Peterson T. Transposon-induced inversions activate gene expression in the maize pericarp. Genetics 2021; 218:iyab062. [PMID: 33905489 PMCID: PMC8225341 DOI: 10.1093/genetics/iyab062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/09/2021] [Indexed: 11/28/2022] Open
Abstract
Chromosomal inversions can have considerable biological and agronomic impacts including disrupted gene function, change in gene expression, and inhibited recombination. Here, we describe the molecular structure and functional impact of six inversions caused by Alternative Transpositions between p1 and p2 genes responsible for floral pigmentation in maize. In maize line p1-wwB54, the p1 gene is null and the p2 gene is expressed in anther and silk but not in pericarp, making the kernels white. By screening for kernels with red pericarp, we identified inversions in this region caused by transposition of Ac and fractured Ac (fAc) transposable elements. We hypothesize that these inversions place the p2 gene promoter near a p1 gene enhancer, thereby activating p2 expression in kernel pericarp. To our knowledge, this is the first report of multiple recurrent inversions that change the position of a gene promoter relative to an enhancer to induce ectopic expression in a eukaryote.
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Affiliation(s)
- Sharu Paul Sharma
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Tao Zuo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Thomas Peterson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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Chatham LA, Juvik JA. Linking anthocyanin diversity, hue, and genetics in purple corn. G3 (BETHESDA, MD.) 2021; 11:jkaa062. [PMID: 33585872 PMCID: PMC8022952 DOI: 10.1093/g3journal/jkaa062] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/30/2020] [Indexed: 01/13/2023]
Abstract
While maize with anthocyanin-rich pericarp (purple corn) is rising in popularity as a source of natural colorant for foods and beverages, information on color range and stability-factors associated with anthocyanin decorations and compositional profiles-is currently limited. Furthermore, to maximize the scalability and meet growing demands, both anthocyanin concentrations and agronomic performance must improve in purple corn varieties. Using the natural anthocyanin diversity present in a purple corn landrace, Apache Red, we generated a population with variable flavonoid profiles-flavanol-anthocyanin condensed forms (0-83%), acylated anthocyanins (2-72%), pelargonidin-derived anthocyanins (5-99%), C-glycosyl flavone co-pigments up to 1904 µg/g, and with anthocyanin content up to 1598 µg/g. Each aspect of the flavonoid profiles was found to play a role in either the resulting extract hue or intensity. With genotyping-by-sequencing of this population, we mapped aspects of the flavonoid profile. Major quantitative trait loci (QTLs) for anthocyanin type were found near loci previously identified only in aleurone-pigmented maize varieties [Purple aleurone1 (Pr1) and Anthocyanin acyltransferase1 (Aat1)]. A QTL near P1 (Pericarp color1) was found for both flavone content and flavanol-anthocyanin condensed forms. A significant QTL associated with peonidin-derived anthocyanins near a candidate S-adenosylmethionine-dependent methyltransferase was also identified, warranting further investigation. Mapping total anthocyanin content produced signals near Aat1, the aleurone-associated bHLH R1 (Colored1), the plant color-associated MYB, Pl1 (Purple plant1), the aleurone-associated recessive intensifier, In1 (Intensifier1), and several previously unidentified candidates. This population represents one of the most anthocyanin diverse pericarp-pigmented maize varieties characterized to date. Moreover, the candidates identified here will serve as branching points for future research studying the genetic and molecular processes determining anthocyanin profile in pericarp.
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Affiliation(s)
- Laura A Chatham
- Department of Crop Sciences, University of Illinois at Urbana Champaign, Champaign, IL 61801, USA
| | - John A Juvik
- Department of Crop Sciences, University of Illinois at Urbana Champaign, Champaign, IL 61801, USA
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Choi JK, Sa KJ, Park DH, Lim SE, Ryu SH, Park JY, Park KJ, Rhee HI, Lee M, Lee JK. Construction of genetic linkage map and identification of QTLs related to agronomic traits in DH population of maize (Zea mays L.) using SSR markers. Genes Genomics 2019; 41:667-678. [PMID: 30953340 DOI: 10.1007/s13258-019-00813-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/26/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND In this study, we used phenotypic and genetic analysis to investigate Double haploid (DH) lines derived from normal corn parents (HF1 and 11S6169). DH technology offers an array of advantages in maize genetics and breeding as follows: first, it significantly shortens the breeding cycle by development of completely homozygous lines in two or three generations; and second, it simplifies logistics, including requiring less time, labor, and financial resources for developing new DH lines compared with the conventional RIL population development process. OBJECTIVES In our study, we constructed a maize genetic linkage map using SSR markers and a DH population derived from a cross of normal corn (HF1) and normal corn (11S6169). METHODS The DH population used in this study was developed by the following methods: we crossed normal corn (HF1) and normal corn (11S6169), which are parent lines of a normal corn cultivar, in 2014; and the next year, the F1 hybrids were crossed with a tropicalized haploid inducer line (TAIL), which is homozygous for the dominant marker gene R1-nj (Nanda and Chase in Crop Sci 6:213-215, 1966), and we harvested seeds of the haploid lines. RESULTS A total of 200 SSR markers were assigned to 10 linkage groups that spanned 1145.4 cM with an average genetic distance between markers of 5.7 cM. 68 SSR markers showed Mendelian segregation ratios in the DH population at a 5% significance threshold. A total of 15 quantitative trait loci (QTLs) for plant height (PH), ear height (EH), ear height ratio (ER), leaf length (LL), ear length (EL), set ear length (SEL), set ear ratio (SER), ear width (EW), 100 kernel weight (100 KW), and cob color (CC) were found in the 121 lines in the DH population. CONCLUSION The results of this study may help to improve the detection and characterization of agronomic traits and provide great opportunities for maize breeders and researchers using a DH population in maize breeding programs.
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Affiliation(s)
- Jae-Keun Choi
- Gangwon-do Agricultural Research and Extension Services, Maize Research Institute, Hongcheon, 25160, Korea.,Department of Medical Biotechnology, Kangwon National University, Chuncheon, 24341, Korea
| | - Kyu Jin Sa
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Dae Hyun Park
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Su Eun Lim
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Si-Hwan Ryu
- Gangwon-do Agricultural Research and Extension Services, Maize Research Institute, Hongcheon, 25160, Korea
| | - Jong Yeol Park
- Gangwon-do Agricultural Research and Extension Services, Maize Research Institute, Hongcheon, 25160, Korea
| | - Ki Jin Park
- Gangwon-do Agricultural Research and Extension Services, Maize Research Institute, Hongcheon, 25160, Korea
| | - Hae-Ik Rhee
- Department of Medical Biotechnology, Kangwon National University, Chuncheon, 24341, Korea
| | - Mijeong Lee
- Department of Anatomy Cell Biology, Kangwon National University School of Medicine, Chuncheon, 24341, Korea
| | - Ju Kyong Lee
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon, 24341, Korea.
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Williams W, Krakowsky M, Scully B, Brown R, Menkir A, Warburton M, Windham G. Identifying and developing maize germplasm with resistance to accumulation of aflatoxins. WORLD MYCOTOXIN J 2015. [DOI: 10.3920/wmj2014.1751] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Efforts to identify maize germplasm with resistance to Aspergillus flavus infection and subsequent accumulation of aflatoxins were initiated by the US Department of Agriculture, Agricultural Research Service at several locations in the late 1970s and early 1980s. Research units at four locations in the south-eastern USA are currently engaged in identification and development of maize germplasm with resistance to A. flavus infection and accumulation of aflatoxins. The Corn Host Plant Resistance Research Unit, Mississippi State, MS, developed procedures for screening germplasm for resistance to A. flavus infection and accumulation of aflatoxins. Mp313E, released in 1990, was the first line released as a source of resistance to A. flavus infection. Subsequently, germplasm lines Mp420, Mp715, Mp717, Mp718, and Mp719 were released as additional sources of resistance. Quantitative trait loci associated with resistance have also been identified in four bi-parental populations. The Crop Protection and Management Research Unit and Crop Genetics and Breeding Research Unit, Tifton, GA, created a breeding population GT-MAS:gk. GT601, GT602, and GT603 were developed from GT-MAS:gk. The Food and Feed Safety Research Unit, New Orleans, LA, in collaboration with the International Institute for Tropical Agriculture used a kernel screening assay to screen germplasm and develop six germplasm lines with resistance to aflatoxins. The Plant Science Research Unit, Raleigh, NC, through the Germplasm Enhancement of Maize (GEM) Project provides to co-operators diverse germplasm that is a valuable source of resistance to A. flavus infection and accumulation of aflatoxins in maize.
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Affiliation(s)
- W.P. Williams
- USDA-ARS, Corn Host Plant Resistance Research Unit, Mississippi State, MS 39762-9555, USA
| | - M.D. Krakowsky
- USDA-ARS, Plant Science Research Unit, North Carolina State University, 1236 Williams Hall, Raleigh, NC 27695-7620, USA
| | - B.T. Scully
- USDA-ARS, Corn Protection and Management Research Unit, 2747 Davis Rd., Tifton, GA 31793, USA
| | - R.L. Brown
- USDA-ARS, Food and Feed Safety Research Unit, Southern Regional Research Center, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA
| | - A. Menkir
- International Institute of Tropical Agriculture, Oyo Rd., PMB 5320, Ibadan, Nigeria
| | - M.L. Warburton
- USDA-ARS, Corn Host Plant Resistance Research Unit, Mississippi State, MS 39762-9555, USA
| | - G.L. Windham
- USDA-ARS, Corn Host Plant Resistance Research Unit, Mississippi State, MS 39762-9555, USA
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Zea mays (L.) P1 locus for cob glume color identified as a post-domestication selection target with an effect on temperate maize genomes. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.cj.2013.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Routaboul JM, Dubos C, Beck G, Marquis C, Bidzinski P, Loudet O, Lepiniec L. Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:3749-64. [PMID: 22442426 PMCID: PMC3388840 DOI: 10.1093/jxb/ers067] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Little is known about the range and the genetic bases of naturally occurring variation for flavonoids. Using Arabidopsis thaliana seed as a model, the flavonoid content of 41 accessions and two recombinant inbred line (RIL) sets derived from divergent accessions (Cvi-0×Col-0 and Bay-0×Shahdara) were analysed. These accessions and RILs showed mainly quantitative rather than qualitative changes. To dissect the genetic architecture underlying these differences, a quantitative trait locus (QTL) analysis was performed on the two segregating populations. Twenty-two flavonoid QTLs were detected that accounted for 11-64% of the observed trait variations, only one QTL being common to both RIL sets. Sixteen of these QTLs were confirmed and coarsely mapped using heterogeneous inbred families (HIFs). Three genes, namely TRANSPARENT TESTA (TT)7, TT15, and MYB12, were proposed to underlie their variations since the corresponding mutants and QTLs displayed similar specific flavonoid changes. Interestingly, most loci did not co-localize with any gene known to be involved in flavonoid metabolism. This latter result shows that novel functions have yet to be characterized and paves the way for their isolation.
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Goettel W, Messing J. Change of gene structure and function by non-homologous end-joining, homologous recombination, and transposition of DNA. PLoS Genet 2009; 5:e1000516. [PMID: 19521498 PMCID: PMC2686159 DOI: 10.1371/journal.pgen.1000516] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 05/13/2009] [Indexed: 11/18/2022] Open
Abstract
An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance. Here, we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct chromosome breakage, transposition, non-homologous end-joining, and homologous recombination events. Such a high-density composition of various mechanisms in a small chromosomal interval exemplifies the evolution of gene regulation and allelic diversity in general. It also illustrates the evolutionary pace of changes in plants, where many of the above mechanisms are of somatic origin. In contrast to animals, somatic alterations can easily be transmitted through meiosis because the germline in plants is contiguous to somatic tissue, permitting the recovery of such chromosomal rearrangements. The analyzed region contains the P1-wr allele, a variant of the genetically well-defined p1 gene, which encodes a Myb-like transcriptional activator in maize. The P1-wr allele consists of eleven nearly perfect P1-wr 12-kb repeats that are arranged in a tandem head-to-tail array. Although a technical challenge to sequence such a structure by shotgun sequencing, we overcame this problem by subcloning each repeat and ordering them based on nucleotide variations. These polymorphisms were also critical for recombination and expression analysis in presence and absence of the trans-acting epigenetic factor Ufo1. Interestingly, chimeras of the p1 and p2 genes, p2/p1 and p1/p2, are framing the P1-wr cluster. Reconstruction of sequence amplification steps at the p locus showed the evolution from a single Myb-homolog to the multi-gene P1-wr cluster. It also demonstrates how non-homologous end-joining can create novel gene fusions. Comparisons to orthologous regions in sorghum and rice also indicate a greater instability of the maize genome, probably due to diploidization following allotetraploidization.
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Affiliation(s)
- Wolfgang Goettel
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
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QTL identification of grain protein concentration and its genetic correlation with starch concentration and grain weight using two populations in maize (Zea mays L.). J Genet 2009; 88:61-7. [DOI: 10.1007/s12041-009-0008-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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