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Studies on Lotus Genomics and the Contribution to Its Breeding. Int J Mol Sci 2022; 23:ijms23137270. [PMID: 35806274 PMCID: PMC9266308 DOI: 10.3390/ijms23137270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Lotus (Nelumbo nucifera), under the Nelumbonaceae family, is one of the relict plants possessing important scientific research and economic values. Because of this, much attention has been paid to this species on both its biology and breeding among the scientific community. In the last decade, the genome of lotus has been sequenced, and several high-quality genome assemblies are available, which have significantly facilitated functional genomics studies in lotus. Meanwhile, re-sequencing of the natural and genetic populations along with different levels of omics studies have not only helped to classify the germplasm resources but also to identify the domestication of selected regions and genes controlling different horticultural traits. This review summarizes the latest progress of all these studies on lotus and discusses their potential application in lotus breeding.
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Cao S, Duan H, Sun Y, Hu R, Wu B, Lin J, Deng W, Li Y, Zheng H. Genome-Wide Association Study With Growth-Related Traits and Secondary Metabolite Contents in Red- and White-Heart Chinese Fir. FRONTIERS IN PLANT SCIENCE 2022; 13:922007. [PMID: 35845628 PMCID: PMC9280351 DOI: 10.3389/fpls.2022.922007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important evergreen coniferous tree species that is widely distributed in many southern provinces of China and has important economic value. The Chinese fir accounts for 1/4 and 1/3 of the total artificial forest area and stock volume, respectively. Red-heart Chinese fir is popular in the market because of its high density and red heartwood. The long-growth cycle hindered the breeding process of Chinese fir, while molecular marker-assisted breeding could accelerate it. However, Chinese fir, a perennial conifer species, has a large genome, which has not yet been published. In this study, the growth-related traits and secondary metabolite contents of red- and white-heart Chinese fir were measured and found to be different between them. There are extremely significant differences among growth-related traits (p < 0.001), but secondary metabolite contents have different correlations due to differences in chemical structure. Moreover, genotype effect analysis of the substantially correlated single nucleotide polymorphisms (SNPs) revealed that most of the loci related to each growth-related traits were different from each other, indicating a type specificity of the genes regulated different growth-related traits. Furthermore, among the loci related to secondary metabolite contents, nine loci associated with multiple metabolite phenotypes such as Marker21022_4, Marker21022_172, Marker24559_31, Marker27425_37, Marker20748_85, Marker18841_115, Marker18841_198, Marker65846_146, and Marker21486_163, suggesting the presence of pleiotropic genes. This study identified the potential SNP markers associated with secondary metabolites in Chinese fir, thus setting the basis for molecular marker-assisted selection.
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Affiliation(s)
- Sen Cao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongjing Duan
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Experimental School Affiliated to Chinese Academy of Sciences, Beijing, China
| | - Yuhan Sun
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ruiyang Hu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, China
| | - Bo Wu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jun Lin
- Longshan State Forest Farm of Lechang, Lechang, China
| | - Wenjian Deng
- Longshan State Forest Farm of Lechang, Lechang, China
| | - Yun Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huiquan Zheng
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
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153
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The first long-read nuclear genome assembly of Oryza australiensis, a wild rice from northern Australia. Sci Rep 2022; 12:10823. [PMID: 35752642 PMCID: PMC9233661 DOI: 10.1038/s41598-022-14893-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
Oryza australiensis is a wild rice native to monsoonal northern Australia. The International Oryza Map Alignment Project emphasises its significance as the sole representative of the EE genome clade. Assembly of the O. australiensis genome has previously been challenging due to its high Long Terminal Repeat (LTR) retrotransposon (RT) content. Oxford Nanopore long reads were combined with Illumina short reads to generate a high-quality ~ 858 Mbp genome assembly within 850 contigs with 46× long read coverage. Reference-guided scaffolding increased genome contiguity, placing 88.2% of contigs into 12 pseudomolecules. After alignment to the Oryza sativa cv. Nipponbare genome, we observed several structural variations. PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. We also report SNV numbers for three additional O. australiensis genotypes based on Illumina re-sequencing. Although genetic similarity reflected geographical separation, the density of SNVs also correlated with our previous report on variations in salinity tolerance. This genome re-confirms the genetic remoteness of the O. australiensis lineage within the O. officinalis genome complex. Assembly of a high-quality genome for O. australiensis provides an important resource for the discovery of critical genes involved in development and stress tolerance.
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154
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Jiang J, Zhang Y, Li Y, Hu C, Xu L, Zhang Y, Wang D, Hong D, Dang X. An Analysis of Natural Variation Reveals That OsFLA2 Controls Flag Leaf Angle in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:906912. [PMID: 35812967 PMCID: PMC9260283 DOI: 10.3389/fpls.2022.906912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Flag leaf angle (FLA) is an important outcrossing trait affecting the hybrid seed production in rice (Oryza sativa L.). Natural variation of FLA has been reported in rice, but the molecular basis for this variation is largely unknown. In this study, we investigated the phenotypic values of FLA in 353 rice natural accessions in six environments, which indicated that there was abundant phenotypic variation. We performed a genome-wide association study on FLA using 1.3 million single nucleotide polymorphisms (SNPs). A total of six quantitative trait loci (QTLs) were identified significantly associated with FLA, of which five were located in previously reported QTLs/genes and one was novel. We identified two causal gene loci for FLA, namely, OsFLA6 and OsFLA2; OsFLA6 was co-localized with the gene OsLIC. In addition, the accessions with large and small FLA values have corresponding high and low OsFLA6 expressions. OsFLA2TT allele could increase significantly the seed setting percentage in hybrid F1 seed production by field experiment. We also confirmed that the allele OsFLA2 TT increased the FLA compared with that of the isogenic line carrying allele OsFLA2 CC by transgenic complementation experiment. The allele frequencies of OsFLA6 GG and OsFLA2 TT decreased gradually with an increase in latitude in the Northern Hemisphere. Our results should facilitate the improvement of FLA of parents of hybrid rice.
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Affiliation(s)
- Jianhua Jiang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yuanqing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yulong Li
- Institute of Crop Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Changmin Hu
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Lei Xu
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ying Zhang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Dezheng Wang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaojing Dang
- Institute of Rice Research, Anhui Academy of Agricultural Sciences, Hefei, China
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155
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Yang B, Chen M, Zhan C, Liu K, Cheng Y, Xie T, Zhu P, He Y, Zeng P, Tang H, Tsugama D, Chen S, Zhang H, Cheng J. Identification of OsPK5 involved in rice glycolytic metabolism and GA/ABA balance for improving seed germination via genome-wide association study. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3446-3461. [PMID: 35191960 PMCID: PMC9162179 DOI: 10.1093/jxb/erac071] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/19/2022] [Indexed: 06/12/2023]
Abstract
Seed germination plays a pivotal role in the plant life cycle, and its precise regulatory mechanisms are not clear. In this study, 19 quantitative trait loci (QTLs) associated with rice seed germination were identified through genome-wide association studies (GWAS) of the following traits in 2016 and 2017: germination rate (GR) at 3, 5, and 7 days after imbibition (DAI) and germination index (GI). Two major stable QTLs, qSG4 and qSG11.1, were found to be associated with GR and GI over 2 continuous years. Furthermore, OsPK5, encoding a pyruvate kinase, was shown to be a crucial regulator of seed germination in rice, and might be a causal gene of the key QTL qSG11.1, on chromosome 11. Natural variation in OsPK5 function altered the activity of pyruvate kinase. The disruption of OsPK5 function resulted in slow germination and seedling growth during seed germination, blocked glycolytic metabolism, caused glucose accumulation, decreased energy levels, and affected the GA/ABA balance. Taken together, our results provide novel insights into the roles of OsPK5 in seed germination, and facilitate its application in rice breeding to improve seed vigour.
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Affiliation(s)
| | | | | | - Kexin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiwen Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Zeng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Haijuan Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
| | - Daisuke Tsugama
- Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo 188-0002, Japan
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing 210095, China
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156
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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157
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Evolution of coastal forests based on a full set of mangrove genomes. Nat Ecol Evol 2022; 6:738-749. [PMID: 35484219 DOI: 10.1038/s41559-022-01744-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/22/2022] [Indexed: 12/11/2022]
Abstract
Genomic studies are now poised to explore whole communities of species. The ~70 species of woody plants that anchor the coastal ecosystems of the tropics, collectively referred to as mangroves, are particularly suited to this exploration. In this study, we de novo sequenced the whole genomes of 32 mangroves, which we combined with other sequences of 30 additional species, comprising almost all mangroves globally. These community-wide genomic data will be valuable for ecology, evolution and biodiversity research. While the data revealed 27 independent origins of mangroves, the total phylogeny shows only modest increases in species number, even in coastal areas of active speciation, suggesting that mangrove extinction is common. A possible explanation for common extinction is the frequent sea-level rises and falls (SLRs and SLFs) documented in the geological record. Indeed, near-extinctions of species with extremely small population size (N) often happened during periods of rapid SLR, as revealed by the genome-wide heterozygosity of almost all mangroves. Reduction in N has possibly been further compounded by population fragmentation and the subsequent accumulation of deleterious mutations, thus pushing mangroves even closer to extinction. Crucially, the impact of the next SLR will be exacerbated by human encroachment into these mangrove habitats, potentially altering the ecosystems of tropical coasts irreversibly.
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158
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Tandukar Z, Chopra R, Frels K, Heim B, Marks MD, Anderson JA. Genetic dissection of seed characteristics in field pennycress via genome-wide association mapping studies. THE PLANT GENOME 2022; 15:e20211. [PMID: 35484973 DOI: 10.1002/tpg2.20211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Field pennycress (Thlaspi arvense L.) is a new winter annual cash cover crop with high oil content and seed yield, excellent winter hardiness, early maturation, and resistance to most pests and diseases. It provides living cover on fallow croplands between summer seasons, and in doing so reduces nutrient leaching into water sources, mitigates soil erosion, and suppresses weed growth. The first ever genome-wide association study (GWAS) was conducted on a pennycress diversity panel to identify marker trait associations with important seed size and composition related traits. The entire population was phenotyped in three total environments over 2 yr, and seed area, length, width, thousand grain weight, total oil, and total protein were measured post-harvest with specialized high-throughput imaging and near-infrared spectroscopy. Basic unbiased linear prediction values were calculated for each trait. Seed size traits tended to have higher entry mean reliabilities (0.76-0.79) compared with oil content (0.51) and protein content (0.37). Genotyping-by-sequencing identified 33,606 high quality genome-wide single nucleotide polymorphism (SNPs) that were coupled with phenotypic data to perform GWAS for seed area, length, width, thousand grain weight, total oil, and total protein content. Fifty-nine total marker-trait associations were identified revealing genomic regions controlling each trait. The significant SNPs explained 0.06-0.18% of the total variance for that trait in our population. A list of candidate genes was identified based on their functional annotations and characterization in other species. Our results confirm that GWAS is an efficient strategy to identify significant marker-trait associations that can be incorporated into marker-assisted selection pipelines to accelerate pennycress breeding progress.
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Affiliation(s)
- Zenith Tandukar
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| | - Ratan Chopra
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, USA
| | - Katherine Frels
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, Lincoln, NE, USA
| | - Brett Heim
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| | - M David Marks
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, USA
| | - James A Anderson
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
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159
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Thummala SR, Guttikonda H, Tiwari S, Ramanan R, Baisakh N, Neelamraju S, Mangrauthia SK. Whole-Genome Sequencing of KMR3 and Oryza rufipogon-Derived Introgression Line IL50-13 (Chinsurah Nona 2/Gosaba 6) Identifies Candidate Genes for High Yield and Salinity Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:810373. [PMID: 35712577 PMCID: PMC9197125 DOI: 10.3389/fpls.2022.810373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
The genomes of an elite rice restorer line KMR3 (salinity-sensitive) and its salinity-tolerant introgression line IL50-13, a popular variety of coastal West Bengal, India, were sequenced. High-quality paired-end reads were obtained for KMR3 (147.6 million) and IL50-13 (131.4 million) with a sequencing coverage of 30X-39X. Scaffolds generated from the pre-assembled contigs of each sequenced genome were mapped separately onto the reference genome of Oryza sativa ssp. japonica cultivar Nipponbare to identify genomic variants in terms of SNPs and InDels. The SNPs and InDels identified for KMR3 and IL50-13 were then compared with each other to identify polymorphic SNPs and InDels unique and common to both the genomes. Functional enrichment analysis of the protein-coding genes with unique InDels identified GO terms involved in protein modification, ubiquitination, deubiquitination, peroxidase activity, and antioxidant activity in IL50-13. Linoleic acid metabolism, circadian rhythm, and alpha-linolenic acid metabolism pathways were enriched in IL50-13. These GO terms and pathways are involved in reducing oxidative damage, thus suggesting their role in stress responses. Sequence analysis of QTL markers or genes known to be associated with grain yield and salinity tolerance showed polymorphism in 20 genes, out of which nine were not previously reported. These candidate genes encoded Nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) domain-containing protein, cyclase, receptor-like kinase, topoisomerase II-associated protein PAT1 domain-containing protein, ion channel regulatory protein, UNC-93 domain-containing protein, subunit A of the heteromeric ATP-citrate lyase, and three conserved hypothetical genes. Polymorphism was observed in the coding, intron, and untranslated regions of the genes on chromosomes 1, 2, 4, 7, 11, and 12. Genes showing polymorphism between the two genomes were considered as sequence-based new candidates derived from Oryza rufipogon for conferring high yield and salinity tolerance in IL50-13 for further functional studies.
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Affiliation(s)
| | | | - Shrish Tiwari
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | | | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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160
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Bai X, Wang X, Wang Y, Wei Y, Fu Y, Rao J, Ma Y, Zeng Z, Li F, Wang M, Zhu S. Genome-Wide Association Study of Six Forage Traits in Ramie ( Boehmeria nivea L. Gaud). PLANTS (BASEL, SWITZERLAND) 2022; 11:1443. [PMID: 35684216 PMCID: PMC9182863 DOI: 10.3390/plants11111443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Genome-wide association study (GWAS) of six forage traits using whole-genome sequencing data generated from 301 ramie accessions found that traits were continuously distributed; the maximum variant coefficient was fresh weight per clump (FWPC) (2019) and individual plant height (IPH) (2019) minimum. Correlation analysis demonstrated that 2019 and 2020 results were similar; all traits were correlated. GWAS analysis demonstrated that six traits exhibited consistent and precise association signals. Of the latter, 104 were significant and detected in 43 genomic regions. By screening forage trait-associated single nucleotide polymorphisms and combining Manhattan map with genome annotation, signals were categorized according to functional annotations. One loci associated with fresh weight per plant (FWP) (chromosome 5; Bnt05G007759), two associated with FWPC (chromosome 13; Bnt13G018582, and Bnt13G018583), and two associated with leaf dry weight per plant (LDWP) and dry weight per plant (DWP) (chromosome 4; Bnt04G005779 and Bnt04G005780), were identified. We describe forage trait candidate genes that are highly correlated with FWP and FWPC; Bnt05G007759 may be involved in nitrogen metabolism, while Bnt13G018582 and Bnt13G018583 may encode TEOSINTE branch 1/CYCLOIDEA/proliferating cytokine 1 (TCP) domains. Bnt04G005779 and Bnt04G005780, which may regulate growth and development, are highly related to LDWP and DWP. These genomic resources will provide a basis for breeding varieties.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Siyuan Zhu
- Correspondence: ; Tel.: +86-138-7580-0740
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161
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Yu Y, Ma L, Wang X, Zhao Z, Wang W, Fan Y, Liu K, Jiang T, Xiong Z, Song Q, Li C, Wang P, Ma W, Xu H, Wang X, Zhao Z, Wang J, Zhang H, Bao Y. Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene, Pb2, Encoding NLR Protein. Int J Mol Sci 2022; 23:ijms23105668. [PMID: 35628477 PMCID: PMC9145240 DOI: 10.3390/ijms23105668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/15/2022] [Accepted: 05/15/2022] [Indexed: 12/24/2022] Open
Abstract
Rice blast is one of the main diseases in rice and can occur in different rice growth stages. Due to the complicated procedure of panicle blast identification and instability of panicle blast infection influenced by the environment, most cloned rice resistance genes are associated with leaf blast. In this study, a rice panicle blast resistance gene, Pb2, was identified by genome-wide association mapping based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel 1 (RDP1) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A genome-wide association study identified 18 panicle blast resistance loci (PBRL) within two years, including 9 reported loci and 2 repeated loci (PBRL2 and PBRL13, PBRL10 and PBRL18). Among them, the repeated locus (PBRL10 and PBRL18) was located in chromosome 11. By haplotype and expression analysis, one of the Nucleotide-binding domain and Leucine-rich Repeat (NLR) Pb2 genes was highly conserved in multiple resistant rice cultivars, and its expression was significantly upregulated after rice blast infection. Pb2 encodes a typical NBS-LRR protein with NB-ARC domain and LRR domain. Compared with wild type plants, the transgenic rice of Pb2 showed enhanced resistance to panicle and leaf blast with reduced lesion number. Subcellular localization of Pb2 showed that it is located on plasma membrane, and GUS tissue-staining observation found that Pb2 is highly expressed in grains, leaf tips and stem nodes. The Pb2 transgenic plants showed no difference in agronomic traits with wild type plants. It indicated that Pb2 could be useful for breeding of rice blast resistance.
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Affiliation(s)
- Yao Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Lu Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Xinying Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Zhi Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Wei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Yunxin Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Kunquan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Tingting Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Ziwei Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Qisheng Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Changqing Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Panting Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Wenjing Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Huanan Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Xinyu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Zijing Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Jianfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
| | - Yongmei Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (Y.Y.); (L.M.); (X.W.); (Z.Z.); (W.W.); (Y.F.); (K.L.); (T.J.); (Z.X.); (Q.S.); (C.L.); (H.X.); (X.W.); (Z.Z.); (J.W.); (H.Z.)
- Correspondence:
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Ćalić I, Groen SC, Choi JY, Joly‐Lopez Z, Hamann E, Natividad MA, Dorph K, Cabral CLU, Torres RO, Vergara GV, Henry A, Purugganan MD, Franks SJ. The influence of genetic architecture on responses to selection under drought in rice. Evol Appl 2022; 15:1670-1690. [PMID: 36330294 PMCID: PMC9624088 DOI: 10.1111/eva.13419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/29/2022] Open
Abstract
Accurately predicting responses to selection is a major goal in biology and important for successful crop breeding in changing environments. However, evolutionary responses to selection can be constrained by such factors as genetic and cross‐environment correlations, linkage, and pleiotropy, and our understanding of the extent and impact of such constraints is still developing. Here, we conducted a field experiment to investigate potential constraints to selection for drought resistance in rice (Oryza sativa) using phenotypic selection analysis and quantitative genetics. We found that traits related to drought response were heritable, and some were under selection, including selection for earlier flowering, which could allow drought escape. However, patterns of selection generally were not opposite under wet and dry conditions, and we did not find individual or closely linked genes that influenced multiple traits, indicating a lack of evidence that antagonistic pleiotropy, linkage, or cross‐environment correlations would constrain selection for drought resistance. In most cases, genetic correlations had little influence on responses to selection, with direct and indirect selection largely congruent. The exception to this was seed mass under drought, which was predicted to evolve in the opposite direction of direct selection due to correlations. Because of this indirect effect on selection on seed mass, selection for drought resistance was not accompanied by a decrease in seed mass, and yield increased with fecundity. Furthermore, breeding lines with high fitness and yield under drought also had high fitness and yield under wet conditions, indicating that there was no evidence for a yield penalty on drought resistance. We found multiple genes in which expression influenced both water use efficiency (WUE) and days to first flowering, supporting a genetic basis for the trade‐off between drought escape and avoidance strategies. Together, these results can provide helpful guidance for understanding and managing evolutionary constraints and breeding stress‐resistant crops.
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Affiliation(s)
- Irina Ćalić
- Department of Biological Sciences Fordham University Bronx NY USA
- Institute of Botany University of Cologne Cologne Germany
| | - Simon C. Groen
- Department of Nematology University of California at Riverside Riverside CA USA
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | - Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | - Zoé Joly‐Lopez
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
- Département de Chimie Université du Québec à Montréal Montréal Québec Canada
| | - Elena Hamann
- Department of Biological Sciences Fordham University Bronx NY USA
- Department of Genetics and Odum School of Ecology University of Georgia Athens GA USA
| | | | - Katherine Dorph
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
| | | | | | - Georgina V. Vergara
- International Rice Research Institute Los Baños Laguna Philippines
- Institute of Crop Science, University of the Philippines Los Baños, 4031 College Laguna Philippines
| | - Amelia Henry
- International Rice Research Institute Los Baños Laguna Philippines
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, Department of Biology New York University New York NY USA
- Center for Genomics and Systems Biology NYU Abu Dhabi Research Institute New York University Abu Dhabi, Saadiyat Island Abu Dhabi United Arab Emirates
| | - Steven J. Franks
- Department of Biological Sciences Fordham University Bronx NY USA
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163
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Mao F, Wu D, Lu F, Yi X, Gu Y, Liu B, Liu F, Tang T, Shi J, Zhao X, Liu L, Ji L. QTL mapping and candidate gene analysis of low temperature germination in rice ( Oryza sativa L.) using a genome wide association study. PeerJ 2022; 10:e13407. [PMID: 35578671 PMCID: PMC9107303 DOI: 10.7717/peerj.13407] [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: 12/20/2021] [Accepted: 04/18/2022] [Indexed: 01/14/2023] Open
Abstract
Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.
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Affiliation(s)
- Feng Mao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, China,Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Depeng Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Fangfang Lu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Xin Yi
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Bin Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Jianxin Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Lilian Ji
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, China
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164
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Cui D, Zhou H, Ma X, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng XW, He H, Han L. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars. PLANT COMMUNICATIONS 2022; 3:100325. [PMID: 35576158 PMCID: PMC9251437 DOI: 10.1016/j.xplc.2022.100325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.
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Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Zhou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Maomao Li
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jianchang Sun
- Institute of Crop Research, Ningxia Academy of Agricultural and Forestry Sciences, Yongning 750105, China
| | - Jin Liu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Guixiu Jin
- Rice Research Institute, Linyi Academy of Agricultural Sciences, Shandong Linyi 276012, China
| | - Xianju Wang
- Rice Research Institute of Liaoning Province, Shenyang 110161, China
| | - Guilan Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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165
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Genetic Analysis of a Collection of Rice Germplasm (Oryza sativa L.) through High-Density SNP Array Provides Useful Information for Further Breeding Practices. Genes (Basel) 2022; 13:genes13050830. [PMID: 35627215 PMCID: PMC9141261 DOI: 10.3390/genes13050830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 11/17/2022] Open
Abstract
Traditional breeding strategies mainly focus on the evaluation of trait performance, but pay less attention to the changing genetic background. A comprehensive understanding of the genetic diversity of germplasms is crucial for the deliberate improvement of specific traits. A collection of 154 highland rice varieties were collected as the initial genetic resource in our breeding program to improve the pathogen resistance and eating and cooking qualities. These varieties were analyzed using a whole-genome SNP array and were clustered into three groups. Further analysis revealed that the favorable alleles of pathogen resistance genes are mostly absent in our collected varieties. However, it showed that most varieties possess favorable alleles of Waxy (Wx) and ALKALI DEGENERATION (ALK), which are able to enhance the eating and cooking qualities. Moreover, only about one fifth of all varieties harbors favorable the allele of fragrance gene Betainealdehyde dehydrogenase (BADH2). Together, these results give an overall view of the genetic constitution of the target traits, which provide useful information for future genetic improvement in breeding practices.
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166
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Wang P, Dong N, Wang M, Sun G, Jia Y, Geng X, Liu M, Wang W, Pan Z, Yang Q, Li H, Wei C, Wang L, Zheng H, He S, Zhang X, Wang Q, Du X. Introgression from Gossypium hirsutum is a driver for population divergence and genetic diversity in Gossypium barbadense. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:764-780. [PMID: 35132720 DOI: 10.1111/tpj.15702] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 05/26/2023]
Affiliation(s)
- Pengpeng Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Na Dong
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, China
| | - Yinhua Jia
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaoli Geng
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Weipeng Wang
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Zhaoe Pan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Qiuyue Yang
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Hongge Li
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Chunyan Wei
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Liru Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | | | - Shoupu He
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qinglian Wang
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
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167
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Wu N, Yao Y, Xiang D, Du H, Geng Z, Yang W, Li X, Xie T, Dong F, Xiong L. A MITE variation-associated heat-inducible isoform of a heat-shock factor confers heat tolerance through regulation of JASMONATE ZIM-DOMAIN genes in rice. THE NEW PHYTOLOGIST 2022; 234:1315-1331. [PMID: 35244216 DOI: 10.1111/nph.18068] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
High temperatures cause huge yield losses in rice. Heat-shock factors (Hsfs) are key transcription factors which regulate the expression of heat stress-responsive genes, but natural variation in and functional characterization of Hsfs have seldom been reported. A significant heat response locus was detected via a genome-wide association study (GWAS) using green leaf area as an indicative trait. A miniature inverted-repeat transposable element (MITE) in the promoter of a candidate gene, HTG3 (heat-tolerance gene on chromosome 3), was found to be significantly associated with heat-induced expression of HTG3 and heat tolerance (HT). The MITE-absent variant has been selected in heat-prone rice-growing regions. HTG3a is an alternatively spliced isoform encoding a functional Hsf, and experiments using overexpression and knockout rice lines showed that HTG3a positively regulates HT at both vegetative and reproductive stages. The HTG3-regulated genes were enriched for heat shock proteins and jasmonic acid signaling. Two heat-responsive JASMONATE ZIM-DOMAIN (JAZ) genes were confirmed to be directly upregulated by HTG3a, and one of them, OsJAZ9, positively regulates HT. We conclude that HTG3 plays an important role in HT through the regulation of JAZs and other heat-responsive genes. The MITE-absent allele may be valuable for HT breeding in rice.
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Affiliation(s)
- Nai Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Yilong Yao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Denghao Xiang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Hao Du
- Institute of Crop science, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zedong Geng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Tingting Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Faming Dong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, No. 1 Shizishan Street, Hongshan District, Wuhan, 430070, China
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168
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You FM, Rashid KY, Zheng C, Khan N, Li P, Xiao J, He L, Yao Z, Cloutier S. Insights into the Genetic Architecture and Genomic Prediction of Powdery Mildew Resistance in Flax ( Linum usitatissimum L.). Int J Mol Sci 2022; 23:ijms23094960. [PMID: 35563347 PMCID: PMC9104541 DOI: 10.3390/ijms23094960] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/29/2022] Open
Abstract
Powdery mildew (PM), caused by the fungus Oidium lini in flax, can cause defoliation and reduce seed yield and quality. To date, one major dominant gene (Pm1) and three quantitative trait loci (QTL) on chromosomes 1, 7 and 9 have been reported for PM resistance. To fully dissect the genetic architecture of PM resistance and identify QTL, a diverse flax core collection of 372 accessions augmented with an additional 75 breeding lines were sequenced, and PM resistance was evaluated in the field for eight years (2010–2017) in Morden, Manitoba, Canada. Genome-wide association studies (GWAS) were performed using two single-locus and seven multi-locus statistical models with 247,160 single nucleotide polymorphisms (SNPs) and the phenotypes of the 447 individuals for each year separately as well as the means over years. A total of 349 quantitative trait nucleotides (QTNs) were identified, of which 44 large-effect QTNs (R2 = 10–30%) were highly stable over years. The total number of favourable alleles per accession was significantly correlated with PM resistance (r = 0.74), and genomic selection (GS) models using all identified QTNs generated significantly higher predictive ability (r = 0.93) than those constructed using the 247,160 genome-wide random SNP (r = 0.69), validating the overall reliability of the QTNs and showing the additivity of PM resistance in flax. The QTNs were clustered on the distal ends of all 15 chromosomes, especially on chromosome 5 (0.4–5.6 Mb and 9.4–16.9 Mb) and 13 (4.7–5.2 Mb). To identify candidate genes, a dataset of 3230 SNPs located in resistance gene analogues (RGAs) was used as input for GWAS, from which an additional 39 RGA-specific QTNs were identified. Overall, 269 QTN loci harboured 445 RGAs within the 200 Kb regions spanning the QTNs, including 45 QTNs located within the RGAs. These RGAs supported by significant QTN/SNP allele effects were mostly nucleotide binding site and leucine-rich repeat receptors (NLRs) belonging to either coiled-coil (CC) NLR (CNL) or toll interleukin-1 (TIR) NLR (TNL), receptor-like kinase (RLK), receptor-like protein kinase (RLP), transmembrane-coiled-coil (TM-CC), WRKY, and mildew locus O (MLO) genes. These results constitute an important genomic tool for resistance breeding and gene cloning for PM in flax.
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Affiliation(s)
- Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Nadeem Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
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169
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Liu Z, Gao S, Zhang H, Xu Z, Qian W. Genome-Wide Association Study Reveals That PvGUX1_1 Is Associated with Pod Stringlessness in Snap Bean (Phaseolus vulgaris L.). BIOLOGY 2022; 11:biology11040611. [PMID: 35453811 PMCID: PMC9024788 DOI: 10.3390/biology11040611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Using 138 snap bean accessions as plant materials, we investigated their suture strings across two years. With the goal of identifying the gene(s) responsible for the formation of suture strings, we conducted a genome-wide association study. A strong association signal was found in a 266.19 kb region on Chr02. Within the region, 23 candidate genes were identified. Importantly, the sequence and gene expression of PvGUX1_1 differed significantly between sutured pods and non-sutured pods. In addition, PvGUX1_1 was also a domesticated locus that diverged from PvGUX1_2 during an early stage. The results obtained in this study can provide important information for the improvement of pod quality in snap beans. Abstract Suture strings are a particularly important pod trait that determine the quality and texture of snap beans (Phaseolus vulgaris L.). The St locus on chromosome 2 has been described as a major locus associated with suture strings. However, the gene and genetic basis underlying this locus remain unknown. Here, we investigated the suture strings of 138 snap bean accessions across two years. A total of 3.66 million single-nucleotide polymorphisms (SNPs) were obtained by deep resequencing. Based on these SNPs, we identified a strong association signal on Chr02 and a promising candidate gene, PvGUX1_1. Further analysis revealed that the 2 bp deletion in the exon of PvGUX1_1 was significantly associated with stringlessness. Comparative mapping indicated that PvGUX1_1 was a domesticated locus and diverged from PvGUX1_2 during an early stage. Our study provides important insights into the genetic mechanism of suture string formation and useful information for snap bean improvement.
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170
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Giordani W, Gama HC, Chiorato AF, Garcia AAF, Vieira MLC. Genome-wide association studies dissect the genetic architecture of seed shape and size in common bean. G3 (BETHESDA, MD.) 2022; 12:jkac048. [PMID: 35218340 PMCID: PMC8982408 DOI: 10.1093/g3journal/jkac048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Seed weight and size are important yield components. Thus, selecting for large seeds has been a key objective in crop domestication and breeding. In common bean, seed shape is also important since it influences industrial processing and plays a vital role in determining the choices of consumers and farmers. In this study, we performed genome-wide association studies on a core collection of common bean accessions to dissect the genetic architecture and identify genomic regions associated with seed morphological traits related to weight, size, and shape. Phenotypic data were collected by high-throughput image-based approaches, and utilized to test associations with 10,362 single-nucleotide polymorphism markers using multilocus mixed models. We searched within genome-associated regions for candidate genes putatively involved in seed phenotypic variation. The collection exhibited high variability for the entire set of seed traits, and the Andean gene pool was found to produce larger, heavier seeds than the Mesoamerican gene pool. Strong pairwise correlations were verified for most seed traits. Genome-wide association studies identified marker-trait associations accounting for a considerable amount of phenotypic variation in length, width, projected area, perimeter, and circularity in 4 distinct genomic regions. Promising candidate genes were identified, e.g. those encoding an AT-hook motif nuclear-localized protein 8, type 2C protein phosphatases, and a protein Mei2-like 4 isoform, known to be associated with seed size and weight regulation. Moreover, the genes that were pinpointed are also good candidates for functional analysis to validate their influence on seed shape and size in common bean and other related crops.
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Affiliation(s)
- Willian Giordani
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Henrique Castro Gama
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | | | - Antonio Augusto Franco Garcia
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Maria Lucia Carneiro Vieira
- Department of Genetics, ‘Luiz de Queiroz’ College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil
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171
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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172
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Krishnamurthy SL, Sharma PC, Dewan D, Lokeshkumar BM, Rathor S, Warraich AS, Vinaykumar NM, Leung H, Singh RK. Genome wide association study of MAGIC population reveals a novel QTL for salinity and sodicity tolerance in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:819-835. [PMID: 35592486 PMCID: PMC9110595 DOI: 10.1007/s12298-022-01174-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 05/24/2023]
Abstract
UNLABELLED The present study was conducted to identify the novel QTLs controlling salinity and sodicity tolerance using indica MAGIC rice population. Phenotyping was carried out in salinity (EC ~ 10 dS/m) and sodicity (pH ~ 9.8) at the seedling stage. Among 391 lines, 43 and 98 lines were found tolerant and moderately tolerant to salinity. For sodicity condition, 2 and 45 lines were showed tolerance and moderately tolerance at seedling stage. MAGIC population was genotyped with the help of genotyping by sequencing (GBS) and filtered 27041SNPs were used for genome wide marker trait association studies. With respect to salinity tolerance, 25 SNPs were distributed on chromosomes 1, 5, 11 and 12, whereas 18 SNPs were mapped on chromosomes 6, 4 and 11 with LOD value of > 3.25 to sodicity tolerance in rice. The candidate gene analysis detected twelve causal genes including SKC1 gene at Saltol region for salinity and six associated genes for sodic stress tolerance. The significant haplotypes responsible for core histone protein coding gene (LOC_Os12g25120) and three uncharacterized protein coding genes (LOC_Os01g20710, LOC_Os01g20870 and LOC_Os12g22020) were identified under saline stress. Likewise, five significant haplotypes coding for ribose 5-phosphate isomerise (LOC_Os04g24140), aspartyl protease (LOC_Os06g15760), aluminum-activated malate transporter (LOC_Os06g15779), OsFBX421-Fbox domain containing protein (LOC_Os11g32940) and one uncharacterized protein (LOC_Os11g32930) were detected for sodic stress tolerance. The identified novel SNPs could be the potential candidates for functional characterization. These candidate genes aid to further understanding of genetic mechanism on salinity and sodicity stress tolerance in rice. The tolerant line could be used in future breeding programme to enhance the salinity and sodicity tolerance in rice. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01174-8.
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Affiliation(s)
| | - P. C. Sharma
- Central Soil Salinity Research Institute, Karnal, India
| | - D. Dewan
- Central Soil Salinity Research Institute, Karnal, India
| | | | - Suman Rathor
- Central Soil Salinity Research Institute, Karnal, India
| | | | | | - Hei Leung
- Division of Genetics and Biotechnology, IRRI, Los Baños, Philippines
| | - R. K. Singh
- Division of Plant Breeding, IRRI, Los Baños, Philippines
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173
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Huang H, Du Y, Long Z, Li Y, Kong W, Wang H, Wei A, Du S, Yang R, Li J, Lin T, Zhang L, Liang B. Fine mapping of a novel QTL CsFSG1 for fruit skin gloss in cucumber ( Cucumis sativus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:25. [PMID: 37309465 PMCID: PMC10248622 DOI: 10.1007/s11032-022-01291-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
Cucumber (Cucumis sativus L.) is an important vegetable crop that is popular with many people. Peel gloss is a highly valued external quality trait that affects the market value of cucumbers, and it directly influences the purchasing psychology of consumers. Nonetheless, the candidate genes and underlying genetic mechanism for this important cucumber trait are not well understood. In this study, we successfully mapped a fruit skin gloss QTL interval to chromosome 3 (26.04-26.14 Mb) using BSA and GWAS methods. Among the eleven candidate genes in the interval, the cytochrome P450 family gene CsCYP86B1 was identified as the candidate for control of fruit skin gloss in cucumber. The expression of CsCYP86B1 in 0-day fruit skin was significantly lower in the low-gloss isogenic line NIL-1334 than in the high-gloss isogenic line NIL-1325. Our findings provide new insights for improving fruit skin gloss in cucumber breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01291-y.
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Affiliation(s)
- Hongyu Huang
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Kernel Cucumber Research Institute, Tianjin, 300192 China
| | - Yuefan Du
- China Agricultural University, Beijing, 100193 China
| | - Zhiqin Long
- China Agricultural University, Beijing, 100193 China
| | - Yuhe Li
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192 China
| | - Weiliang Kong
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Kernel Cucumber Research Institute, Tianjin, 300192 China
| | - Huizhe Wang
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192 China
| | - Aimin Wei
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192 China
| | - Shengli Du
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192 China
| | - Ruihuan Yang
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192 China
| | - Jiawang Li
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Kernel Cucumber Research Institute, Tianjin, 300192 China
| | - Tao Lin
- China Agricultural University, Beijing, 100193 China
| | - Lidong Zhang
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Kernel Cucumber Research Institute, Tianjin, 300192 China
| | - Bin Liang
- China Agricultural University, Beijing, 100193 China
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174
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Zhu F, Ahchige MW, Brotman Y, Alseekh S, Zsögön A, Fernie AR. Bringing more players into play: Leveraging stress in genome wide association studies. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153657. [PMID: 35231821 DOI: 10.1016/j.jplph.2022.153657] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
In order to meet the demand of the burgeoning human population as well as to adapt crops to the enhanced abiotic and biotic stress caused by the global climatic change, breeders focus on identifying valuable genes to improve both crop stress tolerance and crop quality. Recently, with the development of next-generation sequencing methods, millions of high quality single-nucleotide polymorphisms (SNPs) have been made available and genome-wide association studies (GWAS) are widely used in crop improvement studies to identify the associations between genetic variants of genomes and relevant crop agronomic traits. Here, we review classic cases of use of GWAS to identify genetic variants associated with valuable traits such as geographic adaptation, crop quality and metabolites. We discuss the power of stress GWAS to identify further associations including those with genes that are not, or only lowly, expressed during optimal growth conditions. Finally, we emphasize recent demonstrations of the efficiency and accuracy of time-resolved dynamic stress GWAS and GWAS based on genomic gene expression and structural variations, which can be applied to resolve more comprehensively the genetic regulation mechanisms of complex traits.
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Affiliation(s)
- Feng Zhu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Micha Wijesingha Ahchige
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Agustin Zsögön
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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175
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Zhao N, Wang W, Grover CE, Jiang K, Pan Z, Guo B, Zhu J, Su Y, Wang M, Nie H, Xiao L, Guo A, Yang J, Cheng C, Ning X, Li B, Xu H, Adjibolosoo D, Aierxi A, Li P, Geng J, Wendel JF, Kong J, Hua J. Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:691-710. [PMID: 34800075 PMCID: PMC8989498 DOI: 10.1111/pbi.13747] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 05/04/2023]
Abstract
Sea Island cotton (Gossypium barbadense) is the source of the world's finest fibre quality cotton, yet relatively little is understood about genetic variations among diverse germplasms, genes underlying important traits and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. We conducted a genome-wide association study (GWAS) of 15 traits including fibre quality, yield, disease resistance, maturity and plant architecture. The highest number of associated loci was for fibre quality, followed by disease resistance and yield. Using gene expression analyses and VIGS transgenic experiments, we confirmed the roles of five candidate genes regulating four key traits, that is disease resistance, fibre length, fibre strength and lint percentage. Geographical and temporal considerations demonstrated selection for the superior fibre quality (fibre length and fibre strength), and high lint percentage in improving G. barbadense in China. Pedigree selection breeding increased Fusarium wilt disease resistance and separately improved fibre quality and yield. Our work provides a foundation for understanding genomic variation and selective breeding of Sea Island cotton.
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Affiliation(s)
- Nan Zhao
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Weiran Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIAUSA
| | - Kaiyun Jiang
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zhuanxia Pan
- Institute of Cotton ResearchShanxi Agricultural UniversityShanxiChina
| | - Baosheng Guo
- Cotton Research InstituteHebei Academy of Agriculture and Forestry SciencesHebeiChina
| | - Jiahui Zhu
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Ying Su
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Meng Wang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Hushuai Nie
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Li Xiao
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Anhui Guo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jing Yang
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Cheng Cheng
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xinmin Ning
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Bin Li
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Haijiang Xu
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Daniel Adjibolosoo
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Alifu Aierxi
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Pengbo Li
- Institute of Cotton ResearchShanxi Agricultural UniversityShanxiChina
| | - Junyi Geng
- Cotton Research InstituteHebei Academy of Agriculture and Forestry SciencesHebeiChina
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIAUSA
| | - Jie Kong
- Institute of Economic CropsXinjiang Academy of Agricultural SciencesXinjiangChina
| | - Jinping Hua
- Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of Education/College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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Omics: a tool for resilient rice genetic improvement strategies. Mol Biol Rep 2022; 49:5075-5088. [PMID: 35298758 DOI: 10.1007/s11033-022-07189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/24/2022] [Indexed: 10/18/2022]
Abstract
Rice is pivotal pyramid of about half of the world population. Bearing small genome size and worldwide utmost food crop rice has been known as ideal cereal crop for genome research. Currently, decreasing water table and soil fatigue are big challenges and intense consequences in changing climate. Whole sequenced genome of rice sized 389 Mb of which 95% is covered with excellent mapping order. Sequenced rice genome helps in molecular biology and transcriptomics of cereals as it provides whole genome sequence of indica and japonica sub species. Through rice genome sequencing and functional genomics, QTLs or genes, genetic variability and halophyte blocks for agronomic characters were identified which have proved much more useful in molecular breeding and direct selection. There are different numbers of genes or QTLs identified for yield related traits i.e., 6 QTLs/genes for plant architecture, 6 for panicle characteristics, 4 for grain number, 1 gene/QTL for tiller, HGW, grain filling and shattering. QTLS/genes for grain quality, biotic stresses and for abiotic stresses are 7, 23 and 13 respectively. Low yield, inferior quality and susceptibility to biotic and abiotic stresses of a crop is due to narrow genetic background of new evolving rice verities. Wild rice provides genetic resources for improvement of these characters, molecular and genomics tool at different stages can overcome these stresses and improve yield and quality of rice crop.
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177
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Ahmed Z, Khalid M, Ghafoor A, Shah MKN, Raja GK, Rana RM, Mahmood T, Thompson AM. SNP-Based Genome-Wide Association Mapping of Pollen Viability Under Heat Stress in Tropical Zea mays L. Inbred Lines. Front Genet 2022; 13:819849. [PMID: 35368702 PMCID: PMC8966704 DOI: 10.3389/fgene.2022.819849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Global environmental changes with more extreme episodes of heat waves are major threats to agricultural productivity. Heat stress in spring affects the reproductive stage of maize, resulting in tassel blast, pollen abortion, poor pollination, reduced seed set, barren ears and ultimately yield loss. As an aneamophelous crop, maize has a propensity for pollen abortion under heat stress conditions. To overcome the existing challenges of heat stress and pollen abortion, this study utilized a broad genetic base of maize germplasm to identify superior alleles to be utilized in breeding programs. A panel of 375 inbred lines was morpho-physiologically screened under normal and heat stress conditions in two locations across two consecutive planting seasons, 2017 and 2018. The exposure of pollen to high temperature showed drastic decline in pollen germination percentage. The average pollen germination percentage (PGP) at 35 and 45°C was 40.3% and 9.7%, respectively, an average decline of 30.6%. A subset of 275 inbred lines were sequenced using tunable genotyping by sequencing, resulting in 170,098 single nucleotide polymorphisms (SNPs) after filtration. Genome wide association of PGP in a subset of 122 inbred lines resulted in ten SNPs associated with PGP35°C (p ≤ 10−5), nine with PGP45°C (p ≤ 10−6–10−8) and ten SNPs associated with PGP ratio (p ≤ 10−5). No SNPs were found to be in common across PGP traits. The number of favorable alleles possessed by each inbred line for PGP35°C, PGP45°C, and the PGP ratio ranged between 4 and 10, 3–13 and 5–13, respectively. In contrast, the number of negative alleles for these traits ranged between 2 and 8, 3–13 and 3–13, respectively. Genetic mapping of yield (adjusted weight per plant, AWP−1) and flowering time (anthesis-silking interval, ASI) in 275 lines revealed five common SNPs: three shared for AWP−1 between normal and heat stress conditions, one for ASI between conditions, and one SNP, CM007648.1-86615409, was associated with both ASI and AWP−1. Variety selection can be performed based on these favorable alleles for various traits. These marker trait associations identified in the diversity panel can be utilized in breeding programs to improve heat stress tolerance in maize.
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Affiliation(s)
- Zubair Ahmed
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
- Crop Disease Research Institute, National Agricultural Research Center (Pakistan), Islamabad, Pakistan
| | - Maria Khalid
- Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Abdul Ghafoor
- Pakistan Agricultural Research Council, Islamabad, Pakistan
| | - Muhammad Kausar Nawaz Shah
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Ghazala Kaukab Raja
- Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Rashid Mehmood Rana
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Tahir Mahmood
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Addie M Thompson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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178
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Islam MR, Naveed SA, Zhang Y, Li Z, Zhao X, Fiaz S, Zhang F, Wu Z, Hu Z, Fu B, Shi Y, Shah SM, Xu J, Wang W. Identification of Candidate Genes for Salinity and Anaerobic Tolerance at the Germination Stage in Rice by Genome-Wide Association Analyses. Front Genet 2022; 13:822516. [PMID: 35281797 PMCID: PMC8905349 DOI: 10.3389/fgene.2022.822516] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/03/2022] [Indexed: 11/29/2022] Open
Abstract
Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions Xian (Indica) and Geng (Japonica), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (qSGr4a/qCL4c/qRI4d and qAGr4/qSGr4b) and one region on chromosome 10 (qRI10/qCL10/ qSGr10b/qBM10) were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes (OsMT2B and OsTPP7) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene OsMT2B (Os01g0974200) and a major gene OsTPP7 (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing.
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Affiliation(s)
- Mohammad Rafiqul Islam
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shahzad Amir Naveed
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yue Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqing Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Shahid Masood Shah
- Department of Biotechnology, COMSATS University Islamabad-Abbottabad Campus, Abbottabad, Pakistan
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Anhui Agricultural University, Hefei, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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179
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Rashid MAR, Atif RM, Zhao Y, Azeem F, Ahmed HGMD, Pan Y, Li D, Zhao Y, Zhang Z, Zhang H, Li J, Li Z. Dissection of genetic architecture for tiller angle in rice ( Oryza sativa. L) by multiple genome-wide association analyses. PeerJ 2022. [DOI: 10.7717/peerj.12674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background
The rice plant architecture is determined by spatially and temporally domesticated tiller angle. The deeper insight into the genetic mechanism for rice plant architecture will allow more efficient light capture by increasing the planting density, reproducibility, and the ability to survive in a stressful environment.
Methods
In this study, a natural population of 795 genotypes further divided into japonica and indica subpopulations, was evaluated for tiller angle. A significant variation with a wide range was observed. Genome-wide association analysis was performed by the general linear model (GLM), and compressed mix linear model (cMLM) for three populations to disclose the genomic associations. The population principal components and kinship matrix in 1,000 permutations were used to remove the false positives. The candidate genes were evaluated for their functional annotations and specific molecular pathways. The sequencing-based haplotype analysis was further performed to reveal the functional variation among candidate genomic regions.
Results
As a result, 37 significant QTLs with 93 annotated loci were identified. Among the loci, a known tiller angle controlling locus TAC1 was also identified. The introduction of the sequence pooling technique was observed fruitful to screen the 12 significant QTLs with 22 annotated loci. For ten of these loci, the functional variations were identified by haplotype analysis. These results were not only providing a better understanding of the genetic bases of rice plant architecture but also provide significant information for future breeding programs.
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Affiliation(s)
- Muhammad Abdul Rehman Rashid
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- School of Agriculture, Yunnan University, Kunming, Yunnan, China
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Yan Zhao
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong, China
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi, China
| | - Danting Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi, China
| | - Yong Zhao
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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180
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Genome sequencing and genetic analysis of recombinant inbred lines reveals important agronomic traits related loci under different nitrogen fertilization. Mol Biol Rep 2022; 49:4545-4553. [PMID: 35262821 DOI: 10.1007/s11033-022-07298-0] [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: 11/23/2021] [Accepted: 02/23/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND The intensive application of inorganic nitrogen has contributed to increasing the crop yield with the risk of environmental damage. High nitrogen fertilizer requirements are a long-standing problem in japonica cultivation. MATERIALS AND METHODS In the present study, 200 recombinant inbred lines derived from two representative japonica varieties of Japanese and Chinese varieties, Akitakomachi and Liaogeng5, respectively, were planted under different nitrogen fertilization conditions. The relationships among nitrogen fertilization, genetic background, and important agronomic traits were surveyed through the phenotypic investigation and next-generation sequencing. RESULTS The results showed that the yield components of Akitakomachi dramatically decreased along with the nitrogen reduction, whereas those of Liaogeng5 exhibited a slight decrease. The appearance quality and milling quality of both Akitakomachi and Liaogeng5 were improved, especially Liaogeng5. The recombinant inbred lines (RILs) showed similar trends to their parental lines. The QTLs analysis of important agronomic traits detected 17 loci, one QTL clustering located on chromosome 9 that corresponded to the plant height, panicle angle, grain number per panicle, harvest index, and taste value was identified to be synonymous with a previously reported gene, DEP1. The function of DEP1 was verified by a knock-out mutant constructed by CRISPR/Cas9. The dep1 mutant exhibited improved grain quality without severe yield penalty under nitrogen reduction conditions. CONCLUSION The results of the present study provide useful information for the improvement of food security by enhancing nitrogen use efficiency.
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181
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Deng X, Kong W, Sun T, Zhang C, Zhong H, Zhao G, Liu X, Qiang Y, Li Y. Bin mapping-based QTL analyses using three genetic populations derived from indica-japonica crosses uncover multiple grain shape heterosis-related loci in rice. THE PLANT GENOME 2022; 15:e20171. [PMID: 34806841 DOI: 10.1002/tpg2.20171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Exploitation of heterosis between indica and japonica has important significance in scientific research and agriculture application. However, the molecular mechanism of grain shape heterosis in indica-japonica hybrid remains unknown in rice (Oryza sativa L.). To reveal the genetic mechanism of grain shape in indica--japonica hybrid, we constructed a high-generation recombinant inbred line (RIL) population and two testcross hybrid populations derived from the cross of RILs and two cytoplasmic male sterile material (YTA and Z7A) and then performed a bin mapping-based quantitative trait locus (QTL) mapping of multiple grain shape traits, such as grain length (GL), grain width (GW), and grain length-to-width ratio (GLWR). A total of sixteen QTLs and 30 heterosis-related QTLs of grain shape traits were detected. We found that GS3, GS5, and OsPPKL2 were also correlated with grain shape both in RILs and two testcross hybrid populations. Homologous gene analysis emphasized two candidate grain shape-associated genes (LOC_Os06g14260 and LOC_Os04g51950). Our findings uncover multiple grain shape heterosis-related loci and provides a new insight into heterosis mechanism of grain shape in rice.
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Affiliation(s)
- Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Weilong Kong
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Hua Zhong
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Gangqing Zhao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Xuhui Liu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Yalin Qiang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, Ministry of Agriculture, College of Life Sciences, Wuhan Univ., Wuhan, 430072, China
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182
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Kaler AS, Purcell LC, Beissinger T, Gillman JD. Genomic prediction models for traits differing in heritability for soybean, rice, and maize. BMC PLANT BIOLOGY 2022; 22:87. [PMID: 35219296 PMCID: PMC8881851 DOI: 10.1186/s12870-022-03479-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Genomic selection is a powerful tool in plant breeding. By building a prediction model using a training set with markers and phenotypes, genomic estimated breeding values (GEBVs) can be used as predictions of breeding values in a target set with only genotype data. There is, however, limited information on how prediction accuracy of genomic prediction can be optimized. The objective of this study was to evaluate the performance of 11 genomic prediction models across species in terms of prediction accuracy for two traits with different heritabilities using several subsets of markers and training population proportions. Species studied were maize (Zea mays, L.), soybean (Glycine max, L.), and rice (Oryza sativa, L.), which vary in linkage disequilibrium (LD) decay rates and have contrasting genetic architectures. RESULTS Correlations between observed and predicted GEBVs were determined via cross validation for three training-to-testing proportions (90:10, 70:30, and 50:50). Maize, which has the shortest extent of LD, showed the highest prediction accuracy. Amongst all the models tested, Bayes B performed better than or equal to all other models for each trait in all the three crops. Traits with higher broad-sense and narrow-sense heritabilities were associated with higher prediction accuracy. When subsets of markers were selected based on LD, the accuracy was similar to that observed from the complete set of markers. However, prediction accuracies were significantly improved when using a subset of total markers that were significant at P ≤ 0.05 or P ≤ 0.10. As expected, exclusion of QTL-associated markers in the model reduced prediction accuracy. Prediction accuracy varied among different training population proportions. CONCLUSIONS We conclude that prediction accuracy for genomic selection can be improved by using the Bayes B model with a subset of significant markers and by selecting the training population based on narrow sense heritability.
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Affiliation(s)
- Avjinder S Kaler
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Larry C Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Timothy Beissinger
- Department of Crop Science & Center for Integrated Breeding Research, University of Goettingen, 37075, Goettingen, Germany
| | - Jason D Gillman
- Plant Genetics Research Unit, USDA-ARS, 205 Curtis Hall, University of Missouri, Columbia, MO, 65211, USA.
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183
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Genome Wide Association Study Identifies Candidate Genes Related to the Earlywood Tracheid Properties in Picea crassifolia Kom. FORESTS 2022. [DOI: 10.3390/f13020332] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Picea crassifolia Kom. is one of the timber and ecological conifers in China and its wood tracheid traits directly affect wood formation and adaptability under harsh environment. Molecular studies on P. crassifolia remain inadequate because relatively few genes have been associated with these traits. To identify markers and candidate genes that can potentially be used for genetic improvement of wood tracheid traits, we examined 106 clones of P. crassifolia, and investigated phenotypic data for 14 wood tracheid traits before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome wide association study (GWAS). Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the studied traits. We developed 4,058,883 SLAF-tags and 12,275,765 SNP loci, and our analyses identified a total of 96 SNP loci that showed significant correlations with three earlywood tracheid traits using a mixed linear model (MLM). Next, candidate genes were screened in the 100 kb zone (50 kb upstream, 50 kb downstream) of each of the SNP loci, whereby 67 candidate genes were obtained in earlywood tracheid traits, including 34 genes of known function and 33 genes of unknown function. We provide the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in wood traits improvement and candidate genes for the development of earlywood tracheid in P. crassifolia.
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184
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Yu H, Zhang L, Shang X, Peng B, Li Y, Xiao S, Tan Q, Fu Y. Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes. BMC Genomics 2022; 23:120. [PMID: 35144543 PMCID: PMC8832684 DOI: 10.1186/s12864-022-08325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Lentinula edodes (Berk.) is the second most productive mushroom in the world. It contains compounds effective for antiviral, antitumor, antioxidant and immune regulation. Although genomes have previously been reported for this species, a high-quality chromosome-level reference for L. edodes is unavailable. This hinders detailed investigation of population genetics, breeding history of strains and genes related to environmental stress responses. RESULTS A high-quality chromosome-level genome was constructed. We separated a monokaryon from protoplasts of the commercial L. edodes strain L808 and assembled the genome of L. edodes using PacBio long-read and Illumina short-read sequencing, along with the high-throughput chromatin conformation capture (Hi-C) technique. We assembled a 45.87 Mb genome, and 99% of the sequences were anchored onto 10 chromosomes. The contig and scaffold N50 length were 2.17 and 4.94 Mb, respectively. Over 96% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were identified, and 9853 protein-coding genes were predicted. We performed population genome resequencing using 34 wild strains and 65 commercial cultivars of L. edodes originating from China, Japan, the United States and Australia. Based on whole-genome variants, we showed substantial differences in the Chinese wild population, which divided into different branches according to the main areas of their geographical distribution. We also determined the breeding history of L. edodes at the molecular level, and demonstrated that the cultivated strains in China mainly originated from wild strains from China and Northeast Asia. Phenotypic analysis showed that 99 strains exhibited differences on the Cd accumulation. Three significant loci in the of L. edodes genome were identified using the genome-wide association study (GWAS) of Cd accumulation traits. Functional genes associated with Cd accumulation traits were related to DNA ligase and aminoacyl tRNA synthetase, indicating that DNA damage repair and in vivo protein translation may be responses to Cd stress. CONCLUSIONS A high-quality chromosome-level genome and population genetic data of L. edodes provide genetic resources for functional genomic, evolutionary and artificial breeding studies for L. edodes.
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Affiliation(s)
- Hailong Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Lujun Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
| | - Xiaodong Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
| | - Bing Peng
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Yu Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Shijun Xiao
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China.
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, 314000, China.
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China.
| | - Yongping Fu
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China.
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185
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Identification of a Negative Regulator for Salt Tolerance at Seedling Stage via a Genome-wide Association Study of Thai Rice Populations. Int J Mol Sci 2022; 23:ijms23031842. [PMID: 35163767 PMCID: PMC8836775 DOI: 10.3390/ijms23031842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 02/01/2023] Open
Abstract
Salt stress is a major limiting factor in crop production and yield in many regions of the world. The objective of this study was to identify the genes responsible for salt tolerance in Thai rice populations. We performed a genome-wide association study with growth traits, relative water content, and cell membrane stability at the seedling stage, and predicted 25 putative genes. Eleven of them were located within previously reported salt-tolerant QTLs (ST-QTLs). OsCRN, located outside the ST-QTLs, was selected for gene characterization using the Arabidopsis mutant line with T-DNA insertion in the orthologous gene. Mutations in the AtCRN gene led to the enhancement of salt tolerance by increasing the ability to maintain photosynthetic pigment content and relative water content, while the complemented lines with ectopic expression of OsCRN showed more susceptibility to salt stress detected by photosynthesis performance. Moreover, the salt-tolerant rice varieties showed lower expression of this gene than the susceptible rice varieties under salt stress conditions. The study concludes that by acting as a negative regulator, OsCRN plays an important role in salt tolerance in rice.
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186
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Groen SC, Joly-Lopez Z, Platts AE, Natividad M, Fresquez Z, Mauck WM, Quintana MR, Cabral CLU, Torres RO, Satija R, Purugganan MD, Henry A. Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems. THE PLANT CELL 2022; 34:759-783. [PMID: 34791424 PMCID: PMC8824591 DOI: 10.1093/plcell/koab275] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/02/2021] [Indexed: 05/24/2023]
Abstract
Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.
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Affiliation(s)
- Simon C Groen
- Author for correspondence: (S.C.G.), (M.D.P.), (A.H.)
| | | | | | - Mignon Natividad
- International Rice Research Institute, Los Baños, Laguna, Philippines, USA
| | - Zoë Fresquez
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
| | | | | | - Carlo Leo U Cabral
- International Rice Research Institute, Los Baños, Laguna, Philippines, USA
| | - Rolando O Torres
- International Rice Research Institute, Los Baños, Laguna, Philippines, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA
- New York Genome Center, New York, USA
| | | | - Amelia Henry
- Author for correspondence: (S.C.G.), (M.D.P.), (A.H.)
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187
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Verma RK, Chetia SK, Sharma V, Baishya S, Sharma H, Modi MK. GWAS to spot candidate genes associated with grain quality traits in diverse rice accessions of North East India. Mol Biol Rep 2022; 49:5365-5377. [PMID: 35106687 DOI: 10.1007/s11033-021-07113-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022]
Abstract
INTRODUCTION North East (NE) India is the second centre for the origin of rice and is enriched with a diverse collection of traditional rice accessions. These genotypes possess unique traits of breeding interest and are rich in grain nutritional and cooking qualities. Therefore, quantitative trait loci (QTLs)/genes associated with the various quality traits may be identified through genome-wide association studies (GWAS) and used in crop improvement programmes. METHODS AND RESULTS A pool of 526 unique rice accessions from Assam, North East (NE) India were characterized by using 9 grain-quality traits and grouped into 16 clusters. Among these, the highest number of 156 (29.65%) genotypes belongs to diverse phenotypic classes; Sali, Lahi, and Chokuwa were grouped into cluster 6. The first three principal components showed 54.76% of morphological variability with Eigenvalue >1. Genome-wide association studies (GWAS) was performed in 103 rice accessions using 42,446 SNP markers. A total of 11 significant marker-trait associations were detected for 5 grain-quality traits, explaining 0.22-8.86% of phenotypic variation (PV). In-silico mining of QTLs detected 'candidate genes' associated with the quality traits. CONCLUSIONS The phenotypic diversity among the 526 rice accessions of NE India was studied using grain quality traits and grouped into 16 significantly different clusters. The QTLs, or candidate genes identified for various grain quality traits, may be used in breeding programmes for the development of improved rice varieties.
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Affiliation(s)
- Rahul K Verma
- DBT-North East Centre for Agricultural Biotechnology, Jorhat, Assam, 785013, India
| | - S K Chetia
- Regional Agricultural Research Station, Titabar, Assam, 785630, India
| | - Vinay Sharma
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Samindra Baishya
- Department of Biochemistry & Agricultural Chemistry, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Himanshu Sharma
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140306, India
| | - M K Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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188
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Zeng Z, Zhu S, Wang Y, Bai X, Liu C, Chen J, Zhang T, Wei Y, Li F, Bao Z, Yan L, Wang H, Liu T. Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:323-334. [PMID: 34558775 PMCID: PMC8753365 DOI: 10.1111/pbi.13714] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/13/2021] [Indexed: 05/27/2023]
Abstract
Ramie is an important fibre-producing crop in China; however, the genetic basis of its agronomic traits remains poorly understood. We produced a comprehensive map of genomic variation in ramie based on resequencing of 301 landraces and cultivars. Genetic analysis produced 129 signals significantly associated with six fibre yield-related traits, and several genes were identified as candidate genes for respective traits. Furthermore, we found that natural variations in the promoter region of Bnt14G019616 were associated with extremely low fibre abundance, providing the first evidence for the role of pectin methylesterase in fibre growth of plants. Additionally, nucleotide diversity analysis revealed that breeding selection has been markedly focussed on chromosome 9 in which ~ 39.6% sequence underwent selection, where one gibberellin-signalling-repressed DELLA gene showed distinct selection signatures in the cultivars. This study provides insights into the genetic architecture and breeding history of fibre yield traits in ramie. Moreover, the identification of fibre yield-related genetic loci and large-scale genomic variation represent valuable resources for genomics-assisted breeding of this crop.
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Affiliation(s)
- Zheng Zeng
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Siyuan Zhu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Yanzhou Wang
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Xuehua Bai
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Chan Liu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Jianrong Chen
- College of Biological and Environmental EngineeringChangsha UniversityChangshaChina
| | - Ting Zhang
- Shanghai OE Biotech. Co., LtdShanghaiChina
| | - Yiping Wei
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Fu Li
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | - Zhigui Bao
- Shanghai OE Biotech. Co., LtdShanghaiChina
| | - Li Yan
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
| | | | - Touming Liu
- Institute of Bast Fiber CropsChinese Academy of Agricultural SciencesChangshaChina
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189
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Chiteri KO, Jubery TZ, Dutta S, Ganapathysubramanian B, Cannon S, Singh A. Dissecting the Root Phenotypic and Genotypic Variability of the Iowa Mung Bean Diversity Panel. FRONTIERS IN PLANT SCIENCE 2022; 12:808001. [PMID: 35154202 PMCID: PMC8828542 DOI: 10.3389/fpls.2021.808001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Mung bean [Vigna radiata (L.) Wilczek] is a drought-tolerant, short-duration crop, and a rich source of protein and other valuable minerals, vitamins, and antioxidants. The main objectives of this research were (1) to study the root traits related with the phenotypic and genetic diversity of 375 mung bean genotypes of the Iowa (IA) diversity panel and (2) to conduct genome-wide association studies of root-related traits using the Automated Root Image Analysis (ARIA) software. We collected over 9,000 digital images at three-time points (days 12, 15, and 18 after germination). A broad sense heritability for days 15 (0.22-0.73) and 18 (0.23-0.87) was higher than that for day 12 (0.24-0.51). We also reported root ideotype classification, i.e., PI425425 (India), PI425045 (Philippines), PI425551 (Korea), PI264686 (Philippines), and PI425085 (Sri Lanka) that emerged as the top five in the topsoil foraging category, while PI425594 (unknown origin), PI425599 (Thailand), PI425610 (Afghanistan), PI425485 (India), and AVMU0201 (Taiwan) were top five in the drought-tolerant and nutrient uptake "steep, cheap, and deep" ideotype. We identified promising genotypes that can help diversify the gene pool of mung bean breeding stocks and will be useful for further field testing. Using association studies, we identified markers showing significant associations with the lateral root angle (LRA) on chromosomes 2, 6, 7, and 11, length distribution (LED) on chromosome 8, and total root length-growth rate (TRL_GR), volume (VOL), and total dry weight (TDW) on chromosomes 3 and 5. We discussed genes that are potential candidates from these regions. We reported beta-galactosidase 3 associated with the LRA, which has previously been implicated in the adventitious root development via transcriptomic studies in mung bean. Results from this work on the phenotypic characterization, root-based ideotype categories, and significant molecular markers associated with important traits will be useful for the marker-assisted selection and mung bean improvement through breeding.
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Affiliation(s)
- Kevin O. Chiteri
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Talukder Zaki Jubery
- Department of Mechanical Engineering, Iowa State University, Ames, IA, United States
| | - Somak Dutta
- Department of Statistics, Iowa State University, Ames, IA, United States
| | | | - Steven Cannon
- Department of Agronomy, Iowa State University, Ames, IA, United States
- USDA—Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
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190
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Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
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Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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191
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Identification and Allele Combination Analysis of Rice Grain Shape-Related Genes by Genome-Wide Association Study. Int J Mol Sci 2022; 23:ijms23031065. [PMID: 35162989 PMCID: PMC8835367 DOI: 10.3390/ijms23031065] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/30/2022] Open
Abstract
Grain shape is an important agronomic character of rice, which affects the appearance, processing, and the edible quality. Screening and identifying more new genes associated with grain shape is beneficial to further understanding the genetic basis of grain shape and provides more gene resources for genetic breeding. This study has a natural population containing 623 indica rice cultivars. Genome-wide association studies/GWAS of several traits related to grain shape (grain length/GL, grain width/GW, grain length to width ratio/GLWR, grain circumferences/GC, and grain size/grain area/GS) were conducted by combining phenotypic data from four environments and the second-generation resequencing data, which have identified 39 important Quantitative trait locus/QTLs. We analyzed the 39 QTLs using three methods: gene-based association analysis, haplotype analysis, and functional annotation and identified three cloned genes (GS3, GW5, OsDER1) and seven new candidate genes in the candidate interval. At the same time, to effectively utilize the genes in the grain shape-related gene bank, we have also analyzed the allelic combinations of the three cloned genes. Finally, the extreme allele combination corresponding to each trait was found through statistical analysis. This study’s novel candidate genes and allele combinations will provide a valuable reference for future breeding work.
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192
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Peringottillam M, Kunhiraman Vasumathy S, Selvakumar HKK, Alagu M. Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing. Mol Genet Genomics 2022; 297:169-182. [PMID: 35039933 DOI: 10.1007/s00438-021-01844-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/28/2021] [Indexed: 11/24/2022]
Abstract
Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. GBS identified 5856 high-quality SNPs. The structure analysis indicated three subpopulations with the highest probability for population clustering with significant genetic differentiation, confirmed by principal component analysis. The genome-wide LD decay distance was 772 kb, at which the r2 dropped to half its maximum value. The analysis of genetic properties of the identified SNP panel with an average polymorphism information content (PIC) value of 0.22 and a minor allele frequency (MAF) > 0.1 unveiled their efficacy in genome-wide association studies (GWAS). High FST (0.266) and low Nm (0.692) portray a strong genetic differentiation among the rice landraces, complementing the genetic structuring observed in the studied population. Slow LD decay in the rice landraces reflects their self-pollinating behavior and the indirect selection of desired traits by domestication. Moreover, the high LD entails only a minimum number of SNP markers for detecting marker-trait association. The diverse germplasm utilized in this study can be further utilized to disclose genetic variants associated with phenotypic traits and define signatures of selection via GWAS and selective sweep, respectively.
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Affiliation(s)
- Maya Peringottillam
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India
| | - Smitha Kunhiraman Vasumathy
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India
| | - Hari Krishna Kumar Selvakumar
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periye (PO), Kasaragod, Kerala, 671316, India.
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193
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Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton. Commun Biol 2022; 5:60. [PMID: 35039628 PMCID: PMC8764025 DOI: 10.1038/s42003-022-03022-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/21/2021] [Indexed: 02/05/2023] Open
Abstract
Cotton (Gossypium hirsutum L.) fiber is the most important resource of natural and renewable fiber for the textile industry. However, the understanding of genetic components and their genome-wide interactions controlling fiber quality remains fragmentary. Here, we sequenced a multiple-parent advanced-generation inter-cross (MAGIC) population, consisting of 550 individuals created by inter-crossing 11 founders, and established a mosaic genome map through tracing the origin of haplotypes that share identity-by-descent (IBD). We performed two complementary GWAS methods—SNP-based GWAS (sGWAS) and IBD-based haplotype GWAS (hGWAS). A total of 25 sQTLs and 14 hQTLs related to cotton fiber quality were identified, of which 26 were novel QTLs. Two major QTLs detected by both GWAS methods were responsible for fiber strength and length. The gene Ghir_D11G020400 (GhZF14) encoding the MATE efflux family protein was identified as a novel candidate gene for fiber length. Beyond the additive QTLs, we detected prevalent epistatic interactions that contributed to the genetics of fiber quality, pinpointing another layer for trait variance. This study provides new targets for future molecular design breeding of superior fiber quality. Wang and colleagues use a complementary GWAS approach to identify genetic loci associated with cotton fiber quality. Using a multiparent advanced-generation inter-cross population, 26 new QTLs related to cotton fiber quality were found.
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194
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Long R, Zhang F, Zhang Z, Li M, Chen L, Wang X, Liu W, Zhang T, Yu LX, He F, Jiang X, Yang X, Yang C, Wang Z, Kang J, Yang Q. Genome assembly of alfalfa cultivar zhongmu-4 and identification of SNPs associated with agronomic traits. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:14-28. [PMID: 35033678 PMCID: PMC9510860 DOI: 10.1016/j.gpb.2022.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 12/21/2022]
Abstract
Alfalfa (Medicago sativa L.) is the most important legume forage crop worldwide with high nutritional value and yield. For a long time, the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits. We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4, a cultivar widely cultivated in China, and a comprehensive database of genomic variations based on resequencing of 220 germplasms. Approximate 2.74 Gb contigs (N50 of 2.06 Mb), accounting for 88.39% of the estimated genome, were assembled, and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes. A total of 34,922 allelic genes were identified from the allele-aware genome. We observed the expansion of gene families, especially those related to the nitrogen metabolism, and the increase of repetitive elements including transposable elements, which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula. Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe, suggesting that geography may influence alfalfa genetic divergence during local adaption. Genome-wide association studies identified 101 single nucleotide polymorphisms (SNPs) associated with 27 agronomic traits. Two candidate genes were predicted to be correlated with fall dormancy and salt response. We believe that the allele-aware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.
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Affiliation(s)
- Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fan Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99163, United States
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99163, United States
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lin Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenwen Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tiejun Zhang
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant and Germplasm Introduction and Testing Research, Prosser, WA, 99350, United States
| | - Fei He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xueqian Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xijiang Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Changfu Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhen Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Junmei Kang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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195
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Zhao D, Zhang Y, Lu Y, Fan L, Zhang Z, Chai M, Zheng J. Genome sequence and transcriptome of Sorbus pohuashanensis provides insights into population evolution and leaf sunburn response. J Genet Genomics 2022; 49:547-558. [PMID: 34995812 DOI: 10.1016/j.jgg.2021.12.009] [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: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022]
Abstract
Sorbus pohuashanensis is a potential horticulture and medicinal plant, but its genomic and genetic backgrounds remain unknown. Here, we sequenced and assembled the S. pohuashanensis (Hance) Hedl. reference genome using PacBio long reads. Based on the new reference genome, we resequenced a core collection of 22 Sorbus spp. samples, which were divided into 2 groups (G1 and G2) based on phylogenetic and PCA analyses. These phylogenetic clusters were highly consistent with their classification based on leaf shape. Natural hybridization between the G1 and G2 groups was evidenced by a sample (R21) with a highly heterozygous genotype. Nucleotide diversity (π) analysis showed that G1 had a higher diversity than G2 and that G2 originated from G1. During the evolution process, the gene families involved in photosynthesis pathways expanded and the gene families involved in energy consumption contracted. RNA-seq data suggested that flavonoid biosynthesis and heat-shock protein (HSP)-heat-shock factor (HSF) pathways play important roles in protection against sunburn. This study provides new insights into the evolution of Sorbus spp. genomes. In addition, the genomic resources, and the identified genetic variations, especially those related to stress resistance, will help future efforts to produce and breed Sorbus spp.
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Affiliation(s)
- Dongxue Zhao
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Yan Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Yizeng Lu
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, Shandong 250102, China
| | - Liqiang Fan
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Zhibin Zhang
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China
| | - Mao Chai
- Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, Henan 455000, China.
| | - Jian Zheng
- School of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China.
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196
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Alvarez Prado S, Hernández F, Achilli AL, Amelong A. Preparation and Curation of Phenotypic Datasets. Methods Mol Biol 2022; 2481:13-27. [PMID: 35641756 DOI: 10.1007/978-1-0716-2237-7_2] [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] [Indexed: 06/15/2023]
Abstract
Based on case studies, in this chapter we discuss the extent to which the number and identity of quantitative trait loci (QTL) identified from genome-wide association studies (GWAS) are affected by curation and analysis of phenotypic data. The chapter demonstrates through examples the impact of (1) cleaning of outliers, and of (2) the choice of statistical method for estimating genotypic mean values of phenotypic inputs in GWAS. No cleaning of outliers resulted in the highest number of dubious QTL, especially at loci with highly unbalanced allelic frequencies. A trade-off was identified between the risk of false positives and the risk of missing interesting, yet rare alleles. The choice of the statistical method to estimate genotypic mean values also affected the output of GWAS analysis, with reduced QTL overlap between methods. Using mixed models that capture spatial trends, among other features, increased the narrow-sense heritability of traits, the number of identified QTL and the overall power of GWAS analysis. Cleaning and choosing robust statistical models for estimating genotypic mean values should be included in GWAS pipelines to decrease both false positive and false negative rates of QTL detection.
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Affiliation(s)
- Santiago Alvarez Prado
- IFEVA-CONICET, Ciudad de Buenos Aires, Argentina.
- Departamento de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina.
| | - Fernando Hernández
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Ana Laura Achilli
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET), Bahía Blanca, Argentina
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | - Agustina Amelong
- Cátedra de Sistemas de Cultivos Extensivos-GIMUCE, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
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Albert E, Sauvage C. Identification and Validation of Candidate Genes from Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:249-272. [PMID: 35641769 DOI: 10.1007/978-1-0716-2237-7_15] [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] [Indexed: 06/15/2023]
Abstract
Exploiting the statistical associations coming out from a GWAS experiment to identify and validate candidate genes may be potentially difficult and time consuming. To fill the gap between the identification of candidate genes toward their functional validation onto the trait performance, the prioritization of variants underlying the GWAS-associated regions is necessary. In parallel, recent developments in genomics and statistical methods have been achieved notably in human genetic and they are accordingly being adopted in plant breeding toward the study of the genetic architecture of traits to sustain genetic gains. In this chapter, we aim at providing both theoretical and practical aspects underlying three main options including (1) the MetaGWAS analysis, (2) the statistical fine mapping and (3) the integration of functional data toward the identification and validation of candidate genes from a GWAS experiment.
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198
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Yang W, Chen L, Zhao J, Wang J, Li W, Yang T, Dong J, Ma Y, Zhou L, Chen J, Wu W, Zhang S, Liu B. Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures. FRONTIERS IN PLANT SCIENCE 2022; 13:841191. [PMID: 35356125 PMCID: PMC8959774 DOI: 10.3389/fpls.2022.841191] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/02/2022] [Indexed: 05/08/2023]
Abstract
Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. However, the genetic basis of PC in rice is still not well-understood. In this study, a genome-wide association study (GWAS) of PC was performed in a diverse rice collection consisting of 442 accessions using different phenotyping methods in two locations over 2 years. In the whole population consisting of white and colored pericarp rice, a total of 11 quantitative trait loci (QTLs) were identified using two phenotyping methods. Among these QTLs, nine were identified using the phenotypes represented by the presence and absence of pigmentation in pericarp, while 10 were identified using phenotypes of the degree of PC (DPC), in which eight are common QTLs identified using the two phenotyping methods. Using colored rice accessions and phenotypes based on DPC, four QTLs were identified, and they were totally different from the QTLs identified using the whole population, suggesting the masking effects of major genes on minor genes. Compared with the previous studies, 10 out of the 15 QTLs are first reported in this study. Based on the differential expression analysis of the predicted genes within the QTL region by both RNA-seq and real-time PCR (RT-PCR) and the gene functions in previous studies, LOC_Os01g49830, encoding a RAV transcription factor was considered as the candidate gene underlying qPC-1, a novel QTL with a large effect in this study. Our results provide a new insight into the genetic basis of PC in rice and contribute to developing the value-added rice with optimized flavonoid content through molecular breeding.
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Affiliation(s)
- Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Luo Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenhui Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wei Wu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- *Correspondence: Shaohong Zhang,
| | - Bin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
- Guangdong Rice Engineering Laboratory, Guangzhou, China
- Bin Liu,
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199
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Liu S, Qin F. Genome-Wide Association Analyses to Identify SNPs Related to Drought Tolerance. Methods Mol Biol 2022; 2462:201-219. [PMID: 35152391 DOI: 10.1007/978-1-0716-2156-1_16] [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] [Indexed: 06/14/2023]
Abstract
Drought stress is a serious agronomic problem resulting in significant yield losses globally. Breeding cultivars with drought tolerance is an important strategy that can be used to address this problem. Drought tolerance, however, is a complex multigenic trait, making advancements with conventional breeding approaches very challenging. This emphasizes the importance of dissecting the genetics of this trait and the identification and cloning of genes responsible for drought tolerance. With the rapid development of sequencing technologies and analytic methodologies, genome-wide association study (GWAS) has become an important tool for detecting natural variations underlying complex traits in crops. Identified loci can serve as targets for genomic selection or precise editing that enables the molecular design of new cultivars. This chapter describes the pipeline of statistical methods used in GWAS analysis, and covers field design, quality control, population structure control, association tests, and visualization of data. GWAS methodology used to dissect the genetic basis of drought tolerance is presented, and perspectives for optimizing the design and analysis of GWAS are discussed. The provided information serves as a valuable resource for researchers interested in GWAS technology.
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Affiliation(s)
- Shengxue Liu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Feng Qin
- College of Biological Sciences, China Agricultural University, Beijing, China.
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200
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Uchendu K, Njoku DN, Paterne A, Rabbi IY, Dzidzienyo D, Tongoona P, Offei S, Egesi C. Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava. FRONTIERS IN PLANT SCIENCE 2021; 12:770434. [PMID: 34975953 PMCID: PMC8719520 DOI: 10.3389/fpls.2021.770434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.
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Affiliation(s)
- Kelechi Uchendu
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | - Agre Paterne
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Samuel Offei
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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