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Weng WF, Peng Y, Pan X, Yan J, Li XD, Liao ZY, Cheng JP, Gao AJ, Yao X, Ruan JJ, Zhou ML. Adlay, an ancient functional plant with nutritional quality, improves human health. Front Nutr 2022; 9:1019375. [PMID: 36618703 PMCID: PMC9815450 DOI: 10.3389/fnut.2022.1019375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Adlay (Coix lacryma-jobi L.), a crop closed related to maize (Zea mays L.) and sorghum (Sorghum bicolor L.), originated in tropical/subtropical regions of Asia and Africa; southwest China primary center of this plant's origin, evolution and migration. Adlay is a traditional high-value minor crop used for both medicinal and dietary purposes. Adlay has anti-tumor, anti-bacterial, anti-inflammatory, analgesic, blood sugar-lowering, and blood lipid-lowering effects. To clarify the main bioactive components and phytochemical compounds and to fully explore their utility, this review summarizes the research done on the main functional ingredients of adlay, including amino acids and proteins, oils, vitamins and minerals, polysaccharides, and polyphenols. This study also highlighted the application of genome sequencing to tailor nutrient-rich adlay cultivars and nutraceutical product development. Additionally, the acquisition of high-density genomic data combined with next-generation phenotypic analysis will undoubtedly improve our understanding of the potential genetic regulation of adlay nutraceutical traits. This review provides new insights and ideas for the research of adlay in comparison and evolutionary genomics, and a useful reference for molecular breeding and genetic improvement of this important minor crop.
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Affiliation(s)
- Wen F. Weng
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Yan Peng
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Xin Pan
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing in Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Xiang D. Li
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
| | - Zhi Y. Liao
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
| | - Jian P. Cheng
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - An J. Gao
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Xin Yao
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Jing J. Ruan
- College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Mei L. Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Huda N, Li X, Jahan T, He Y, Guan C, Zhang K, Gao A, Georgiev MI, Zhou M. Acceleration of the genetic gain for nutraceutical improvement of adlay ( Coix L.) through genomic approaches: current status and future prospects. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2022.2067175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nurul Huda
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangdong Li
- Southwest Guizhou Institute of Karst Regional Development, Xingyi, Guizhou, China
| | - Tanzim Jahan
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yuqi He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Guan
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ainong Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Milen I. Georgiev
- Laboratory of Metabolomics, Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Meiliang Zhou
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya 572024, China
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Kang SH, Kim B, Choi BS, Lee HO, Kim NH, Lee SJ, Kim HS, Shin MJ, Kim HW, Nam K, Kang KD, Kwon SJ, Oh TJ, Lee SC, Kim CK. Genome Assembly and Annotation of Soft-Shelled Adlay ( Coix lacryma-jobi Variety ma-yuen), a Cereal and Medicinal Crop in the Poaceae Family. FRONTIERS IN PLANT SCIENCE 2020; 11:630. [PMID: 32528499 PMCID: PMC7247446 DOI: 10.3389/fpls.2020.00630] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/23/2020] [Indexed: 05/21/2023]
Abstract
Coix lacryma-jobi, also called adlay or Job's tears, is an annual herbal plant belonging to the Poaceae family that has been cultivated as a cereal and medicinal crop in Asia. Despite its importance, however, genomic resources for better understanding this plant species at the molecular level and informing improved breeding strategies remain limited. To address this, we generated a draft genome of the C. lacryma-jobi variety ma-yuen (soft-shelled adlay) Korean cultivar, Johyun, by de novo assembly, using PacBio and Illumina sequencing data. A total of 3,362 scaffold sequences, 1.28 Gb in length, were assembled, representing 82.1% of the estimated genome size (1.56 Gb). Genome completeness was confirmed by the presence of 91.4% of the BUSCO angiosperm genes and mapping ratio of 98.3% of Illumina paired-end reads. We found that approximately 77.0% of the genome is occupied by repeat sequences, most of which are Gypsy and Copia-type retrotransposons, and evidence-based genome annotation predicts 39,574 protein-coding genes, 85.5% of which were functionally annotated. We further predict that soft-shelled adlay diverged from a common ancestor with sorghum 9.0-11.2 MYA. Transcriptome profiling revealed 3,988 genes that are differentially expressed in seeds relative to other tissues, of which 1,470 genes were strongly up-regulated in seeds and the most enriched Gene Ontology terms were assigned to carbohydrate and protein metabolism. In addition, we identified 76 storage protein genes including 18 seed-specific coixin genes and 13 candidate genes involved in biosynthesis of benzoxazinoids (BXs) including coixol, a unique BX compound found in C. lacryma-jobi species. The characterization of those genes can further our understanding of unique traits of soft-shelled adlay, such as high seed protein content and medicinal compound biosynthesis. Taken together, our genome sequence data will provide a valuable resource for molecular breeding and pharmacological study of this plant species.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan, South Korea
| | | | | | | | | | | | | | | | | | | | - Soo-Jin Kwon
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan, South Korea
| | - Sang-Choon Lee
- Phyzen Co., Seongnam, South Korea
- *Correspondence: Sang-Choon Lee,
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
- Chang-Kug Kim,
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Cai Z, Liu H, He Q, Pu M, Chen J, Lai J, Li X, Jin W. Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping. BMC Genomics 2014; 15:1025. [PMID: 25425126 PMCID: PMC4256728 DOI: 10.1186/1471-2164-15-1025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 11/19/2014] [Indexed: 02/07/2023] Open
Abstract
Abstract Background Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9–11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have been reported for C. aquatica Roxb. One sterile cytotype (2n = 30) closely related to C. aquatica has been recently found in Guangxi of China. This putative hybrid has been named C. aquatica HG (Hybrid Guangxi). The genome composition and the evolutionary history of C. lacryma-jobi and C. aquatica HG are largely unclear. Results About 76% of the genome of C. lacryma-jobi and 73% of the genome of C. aquatica HG are repetitive DNA sequences as shown by low coverage genome sequencing followed by similarity-based cluster analysis. In addition, long terminal repeat (LTR) retrotransposable elements are dominant repetitive sequences in these two genomes, and the proportions of many repetitive sequences in whole genome varied greatly between the two species, indicating evolutionary divergence of them. We also found that a novel 102 bp variant of centromeric satellite repeat CentX and two other satellites only appeared in C. aquatica HG. The results from FISH analysis with repeat probe cocktails and the data from chromosomes pairing in meiosis metaphase showed that C. lacryma-jobi is likely a diploidized paleotetraploid species and C. aquatica HG is possibly a recently formed hybrid. Furthermore, C. lacryma-jobi and C. aquatica HG shared more co-existing repeat families and higher sequence similarity with Sorghum than with Zea. Conclusions The composition and abundance of repetitive sequences are divergent between the genomes of C. lacryma-jobi and C. aquatica HG. The results from fine karyotyping analysis and chromosome pairing suggested diploidization of C. lacryma-jobi during evolution and C. aquatica HG is a recently formed hybrid. The genome-wide comparison of repetitive sequences indicated that the repeats in Coix were more similar to those in Sorghum than to those in Zea, which is consistent with the phylogenetic relationship reported by previous work. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1025) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Weiwei Jin
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, Coordinated Research Center for Crop Biology, China Agricultural University, Beijing 100193, China.
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Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives. Genetics 2013; 195:723-37. [PMID: 24037269 DOI: 10.1534/genetics.113.157115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.
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Zhou L, Huang B, Meng X, Wang G, Wang F, Xu Z, Song R. The amplification and evolution of orthologous 22-kDa α-prolamin tandemly arrayed genes in coix, sorghum and maize genomes. PLANT MOLECULAR BIOLOGY 2010; 74:631-643. [PMID: 20938800 DOI: 10.1007/s11103-010-9705-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 09/30/2010] [Indexed: 05/30/2023]
Abstract
Tandemly arrayed genes (TAGs) account for about one-third of the duplicated genes in eukaryotic genomes. They provide raw genetic material for biological evolution, and play important roles in genome evolution. The 22-kDa prolamin genes in cereal genomes represent typical TAG organization, and provide the good material to investigate gene amplification of TAGs in closely related grass genomes. Here, we isolated and sequenced the Coix 22-kDa prolamin (coixin) gene cluster (283 kb), and carried out a comparative analysis with orthologous 22-kDa prolamin gene clusters from maize and sorghum. The 22-kDa prolamin gene clusters descended from orthologous ancestor genes, but underwent independent gene amplification paths after the separation of these species, therefore varied dramatically in sequence and organization. Our analysis indicated that the gene amplification model of 22-kDa prolamin gene clusters can be divided into three major stages. In the first stage, rare gene duplications occurred from the ancestor gene copy accidentally. In the second stage, rounds of gene amplification occurred by unequal crossing over to form tandem gene array(s). In the third stage, gene array was further diverged by other genomic activities, such as transposon insertions, segmental rearrangements, etc. Unlike their highly conserved sequences, the amplified 22-kDa prolamin genes diverged rapidly at their expression capacities and expression levels. Such processes had no apparent correlation to age or order of amplified genes within TAG cluster, suggesting a fast evolving nature of TAGs after gene amplification. These results provided insights into the amplification and evolution of TAG families in grasses.
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Affiliation(s)
- Liangliang Zhou
- Shanghai Key Laboratory of Bio-energy Crops, School of Life Sciences, Shanghai University, 99 Shangda Road, 200444, Shanghai, People's Republic of China
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