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Zhang L, Xu J, Ding Y, Cao N, Gao X, Feng Z, Li K, Cheng B, Zhou L, Ren M, Tao Y, Zou G. GWAS of grain color and tannin content in Chinese sorghum based on whole-genome sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:77. [PMID: 36952041 PMCID: PMC10036430 DOI: 10.1007/s00122-023-04307-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Seventy-three QTL related to grain color and tannin content were identified in Chinese sorghum accessions, and a new recessive allelic variant of TAN2 gene was discovered. Sorghum is mainly used for brewing distilled liquors in China. Since grain tannins play an important role in liquor brewing, accurately understanding the relationship between grain color and tannin content can provide basis for selection standards of tannin sorghum. We resequenced a panel of 242 Chinese sorghum accessions and performed population structure and genome-wide association study (GWAS) to identify quantitative trait locus (QTL) affecting pericarp color, testa pigment, and tannin content. Phylogenetic analysis, principal component analysis (PCA), and admixture model were used to infer population structure. Two distinct genetic sub-populations were identified according to their corresponding northern and southern geographic origin. To investigate the genetic basis of natural variation in sorghum grain color, GWAS with 2,760,264 SNPs was conducted in four environments using multiple models (Blink, FarmCPU, GLM, and MLM). Seventy-three QTL were identified to be associated for the color of exocarp, mesocarp, testa, and tannin content on all chromosomes except chromosome 5, of which 47 might be novel QTL. Some important QTL were found to colocalize with orthologous genes in the flavonoid biosynthetic pathway from other plants, including orthologous of Arabidopsis (Arabidopsis thaliana) TT2, TT7, TT12, TT16 and AT5G41220 (GST), as well as orthologous of rice (Oryza sativa) MYB61 and OsbHLH025. Our investigation of the variation in grain color and tannin content in Chinese sorghum germplasm may help guide future sorghum breeding for liquor brewing.
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Affiliation(s)
- Liyi Zhang
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China.
| | - Jianxia Xu
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Yanqing Ding
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Ning Cao
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Xu Gao
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Zhou Feng
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Kuiying Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Bing Cheng
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Lengbo Zhou
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Mingjian Ren
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Zhejiang Key Laboratory of Digital Dry Land Crops, Hangzhou, 310021, China
| | - Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Zhejiang Key Laboratory of Digital Dry Land Crops, Hangzhou, 310021, China.
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John Martin JJ, Yarra R, Wei L, Cao H. Oil Palm Breeding in the Modern Era: Challenges and Opportunities. PLANTS 2022; 11:plants11111395. [PMID: 35684168 PMCID: PMC9183044 DOI: 10.3390/plants11111395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Oil palm, a cross-pollinated crop with long generation time, poses a lot of challenges in achieving sustainable oil palm with high yield and quality. The African oil palm (Elaeis guineensis Jacq.) is the most productive and versatile oil-yielding crop in the world, producing more than any other oil-yielding crop. Despite recent challenges, such as stress tolerance, superior oil quality, disease tolerance, and the need for new market niches, there is a growing need to explore and develop new varieties with high yield potential and the genetic diversity required to maintain oil palm yield stability. Breeding is an indispensable part of producing high-quality planting materials to increase oil palm yield. Biotechnological technologies have transformed conventional plant breeding approaches by introducing novel genotypes for breeding. Innovative pre-breeding and breeding approaches, such as identifying candidate genes in wild or land races using genomics tools, can pave the way for genetic improvement in oil palm. In this review, we highlighted the modern breeding tools, including genomics, marker-assisted breeding, genetic engineering, and genome editing techniques in oil palm crops, and we explored certain concerns connected to the techniques and their applications in practical breeding.
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Affiliation(s)
- Jerome Jeyakumar John Martin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Lu Wei
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
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Yarra R, Cao H, Jin L, Mengdi Y, Zhou L. CRISPR/Cas mediated base editing: a practical approach for genome editing in oil palm. 3 Biotech 2020; 10:306. [PMID: 32566443 DOI: 10.1007/s13205-020-02302-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/11/2020] [Indexed: 10/24/2022] Open
Abstract
The improvement of the yield and quality of oil palm via precise genome editing has been indispensable goal for oil palm breeders. Genome editing via the CRISPR/Cas9 (CRISPR-associated protein 9) system, ZFN (zinc finger nucleases) and TALEN (transcription activator-like effector nucleases) has flourished as an efficient technology for precise target modifications in the genomes of various crops. Among the genome editing technologies, base editing approach has emerged as novel technology that could generate single base changes i.e. irreversible conversion of one target base in to other in a programmable manner. A base editor (adenine or cytosine) is a fusion of catalytically inactive CRISPR-Cas9 domain (Cas9 variants) and cytosine or adenosine deaminase domain that introduces desired point mutations. However, till date no such genetic modifications have ever been developed in oil palm via base editing technology. Precise genome editing via base editing approach can be a challenging task in oil palm due to its complex genome as well as difficulties in tissue culture and genetic transformation methods. However, availability of whole genome sequencing data in oil palm provides a platform for developing the base editing technology. Here, we briefly review the potential application and future implications of base editing technology for the genetic improvement of oil palm.
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Construction of a high density linkage map in Oil Palm using SPET markers. Sci Rep 2020; 10:9998. [PMID: 32561804 PMCID: PMC7305113 DOI: 10.1038/s41598-020-67118-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/01/2020] [Indexed: 11/08/2022] Open
Abstract
A high-density genetic linkage map from a controlled cross of two oil palm (Elaeis guineensis) genotypes was constructed based on Single Primer Enrichment Technology (SPET) markers. A 5K panel of hybridization probes were used for this purpose which was derived from previously developed SNP primers in oil palm. Initially, 13,384 SNPs were detected which were reduced to 13,073 SNPs after filtering for only bi-allelic SNP. Around 75% of the markers were found to be monomorphic in the progeny, reducing the markers left for linkage mapping to 3,501. Using Lep-MAP3 software, a linkage map was constructed which contained initially 2,388 markers and had a total length of 1,370 cM. In many cases several adjacent SNP were located on the same locus, due to missing recombination events between them, leading to a total of 1,054 loci on the 16 LG. Nevertheless, the marker density of 1.74 markers per cM (0.57 cM/marker) should allow the detection of QTLs in the future. This study shows that cost efficient SPET markers are suitable for linkage map construction in oil palm and probably, also in other species.
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Mozzon M, Foligni R, Mannozzi C. Current Knowledge on Interspecific Hybrid Palm Oils as Food and Food Ingredient. Foods 2020; 9:E631. [PMID: 32422962 PMCID: PMC7278620 DOI: 10.3390/foods9050631] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/09/2020] [Accepted: 05/10/2020] [Indexed: 12/13/2022] Open
Abstract
The consumers' opinion concerning conventional palm (Elaeis guineensis) oil is negatively affected by environmental and nutritional issues. However, oils extracted from drupes of interspecific hybrids Elaeis oleifera × E. guineensis are getting more and more interest, due to their chemical and nutritional properties. Unsaturated fatty acids (oleic and linoleic) are the most abundant constituents (60%-80% of total fatty acids) of hybrid palm oil (HPO) and are mainly acylated in position sn-2 of the glycerol backbone. Carotenes and tocotrienols are the most interesting components of the unsaponifiable matter, even if their amount in crude oils varies greatly. The Codex Committee on Fats and Oils recently provided HPO the "dignity" of codified fat substance for human consumption and defined the physical and chemical parameters for genuine crude oils. However, only few researches have been conducted to date on the functional and technological properties of HPO, thus limiting its utilization in food industry. Recent studies on the nutritional effects of HPO softened the initial enthusiasm about the "tropical equivalent of olive oil", suggesting that the overconsumption of HPO in the most-consumed processed foods should be carefully monitored.
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Affiliation(s)
| | - Roberta Foligni
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche 10, 60131 Ancona, Italy;
| | - Cinzia Mannozzi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche 10, 60131 Ancona, Italy;
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