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Sallam A, Awadalla RA, Elshamy MM, Börner A, Heikal YM. Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population. Comput Struct Biotechnol J 2024; 23:870-882. [PMID: 38356657 PMCID: PMC10864764 DOI: 10.1016/j.csbj.2024.01.020] [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: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.
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Affiliation(s)
- Ahmed Sallam
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, 71526 Assiut, Egypt
| | - Rawan A. Awadalla
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Maha M. Elshamy
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
| | - Andreas Börner
- Resources Genetics and Reproduction, Department GenBank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben D-06466 Stadt Seeland, Germany
| | - Yasmin M. Heikal
- Botany Department, Faculty of Science, Mansoura University, 35516 Mansoura, Egypt
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Botkin J, Medina C, Park S, Poudel K, Cha M, Lee Y, Prom LK, Curtin SJ, Xu Z, Ahn E. Analyzing Medicago spp. seed morphology using GWAS and machine learning. Sci Rep 2024; 14:17588. [PMID: 39080407 PMCID: PMC11289399 DOI: 10.1038/s41598-024-67790-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Alfalfa is widely recognized as an important forage crop. To understand the morphological characteristics and genetic basis of seed morphology in alfalfa, we screened 318 Medicago spp., including 244 Medicago sativa subsp. sativa (alfalfa) and 23 other Medicago spp., for seed area size, length, width, length-to-width ratio, perimeter, circularity, the distance between the intersection of length & width (IS) and center of gravity (CG), and seed darkness & red-green-blue (RGB) intensities. The results revealed phenotypic diversity and correlations among the tested accessions. Based on the phenotypic data of M. sativa subsp. sativa, a genome-wide association study (GWAS) was conducted using single nucleotide polymorphisms (SNPs) called against the Medicago truncatula genome. Genes in proximity to associated markers were detected, including CPR1, MON1, a PPR protein, and Wun1(threshold of 1E-04). Machine learning models were utilized to validate GWAS, and identify additional marker-trait associations for potentially complex traits. Marker S7_33375673, upstream of Wun1, was the most important predictor variable for red color intensity and highly important for brightness. Fifty-two markers were identified in coding regions. Along with strong correlations observed between seed morphology traits, these genes will facilitate the process of understanding the genetic basis of seed morphology in Medicago spp.
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Affiliation(s)
- Jacob Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Cesar Medina
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sunchung Park
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture- Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA
| | - Kabita Poudel
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Minhyeok Cha
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Yoonjung Lee
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Louis K Prom
- United States Department of Agriculture- Agricultural Research Service, Southern Plains Agricultural Research Center, 2765 F & B Road, College Station, TX, 77845, USA
| | - Shaun J Curtin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Plant Science Research Unit, United States Department of Agriculture- Agricultural Research Service, St. Paul, MN, 55108, USA
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, 55108, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, 55108, USA
| | - Zhanyou Xu
- Plant Science Research Unit, United States Department of Agriculture- Agricultural Research Service, St. Paul, MN, 55108, USA.
| | - Ezekiel Ahn
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture- Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA.
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An Y, Xia X, Zhang X, Liu L, Jiang S, Jing T, Zhang F. Genome-wide identification of the sorghum OVATE gene family and revelation of its expression characteristics in sorghum seeds and leaves. Sci Rep 2024; 14:15123. [PMID: 38956272 PMCID: PMC11219837 DOI: 10.1038/s41598-024-66103-z] [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] [Received: 01/09/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
The OVATE gene family plays an important role in regulating the development of plant organs and resisting stress, but its expression characteristics and functions in sorghum have not been revealed. In this study, we identified 26 OVATE genes in the sorghum BTx623 genome, which were divided into four groups and distributed unevenly across 9 chromosomes. Evolutionary analysis showed that after differentiation between sorghum and Arabidopsis, the OVATE gene family may have experienced unique expansion events, and all OVATE family members were negatively selected. Transcriptome sequencing and RT-qPCR results showed that OVATE genes in sorghum showed diverse expression characteristics, such as gene SORBl_3001G468900 and SORBl_3009G173400 were significantly expressed in seeds, while SORBI_3005G042700 and SORBI_3002G417700 were only highly expressed in L1. Meantime, in the promoter region, a large number of hormone-associated cis-acting elements were identified, and these results suggest that members of the OVATE gene family may be involved in regulating specific development of sorghum leaves and seeds. This study improves the understanding of the OVATE gene family of sorghum and provides important clues for further exploration of the function of the OVATE gene family.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Xiaobo Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoqin Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Li Liu
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Sixia Jiang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China.
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China.
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Htwe YM, Shi P, Zhang D, Li Z, Yu Q, Wang Y. GWAS determined genetic loci associated with callus induction in oil palm tissue culture. PLANT CELL REPORTS 2024; 43:128. [PMID: 38652306 DOI: 10.1007/s00299-024-03221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE GWAS identified six loci at 25 kb downstream of WAK2, a crucial gene for cell wall and callus formation, enabling development of a SNP marker for enhanced callus induction potential. Efficient callus induction is vital for successful oil palm tissue culture, yet identifying genomic loci and markers for early detection of genotypes with high potential of callus induction remains unclear. In this study, immature male inflorescences from 198 oil palm accessions (dura, tenera and pisifera) were used as explants for tissue culture. Callus induction rates were collected at one-, two- and three-months after inoculation (C1, C2 and C3) as phenotypes. Resequencing generated 11,475,258 high quality single nucleotide polymorphisms (SNPs) as genotypes. GWAS was then performed, and correlation analysis revealed a positive association of C1 with both C2 (R = 0.81) and C3 (R = 0.50), indicating that C1 could be used as the major phenotype for callus induction rate. Therefore, only significant SNPs (P ≤ 0.05) in C1 were identified to develop markers for screening individuals with high potential of callus induction. Among 21 significant SNPs in C1, LD block analysis revealed six SNPs on chromosome 12 (Chr12) potentially linked to callus formation. Subsequently, 13 SNP markers were identified from these loci and electrophoresis results showed that marker C-12 at locus Chr12_12704856 can be used effectively to distinguish the GG allele, which showed the highest probability (69%) of callus induction. Furthermore, a rapid SNP variant detection method without electrophoresis was established via qPCR-based melting curve analysis. Our findings facilitated marker-assisted selection for specific palms with high potential of callus induction using immature male inflorescence as explant, aiding ortet palm selection in oil palm tissue culture.
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Affiliation(s)
- Yin Min Htwe
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Peng Shi
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Dapeng Zhang
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Zhiying Li
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Qun Yu
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Yong Wang
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.
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Ahn E, Prom LK, Park S, Hu Z, Magill CW. Genome-Wide Association Analysis Uncovers Genes Associated with Resistance to Head Smut Pathotype 5 in Senegalese Sorghum Accessions. PLANTS (BASEL, SWITZERLAND) 2024; 13:977. [PMID: 38611506 PMCID: PMC11013943 DOI: 10.3390/plants13070977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
A newly documented pathotype 5 of the soil-borne fungus Sporisorium reilianum, causing head smut in sorghum, was tested against 153 unexplored Senegalese sorghum accessions. Among the 153 sorghum accessions tested, 63 (41%) exhibited complete resistance, showing no signs of infection by the fungus. The remaining 90 accessions (59%) displayed varying degrees of susceptibility. Sorghum responses against S. reilianum were explored to analyze the potential link with previously known seed morphology-related traits and new phenotype data from 59 lines for seed weight. A genome-wide association study (GWAS) screened 297,876 SNPs and identified highly significant associations (p < 1 × 10-5) with head smut resistance in sorghum. By mapping these significant SNPs to the reference genome, this study revealed 35 novel candidate defense genes potentially involved in disease resistance.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Louis K. Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA;
| | - Sunchung Park
- USDA-ARS Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Zhenbin Hu
- USDA-ARS Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Clint W. Magill
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, USA
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An Y, Xia X, Zheng H, Yu S, Jing T, Zhang F. Multi-genome comprehensive identification of SSR/SV and development of molecular markers database to serve Sorghum bicolor (L.) breeding. BMC Genom Data 2023; 24:62. [PMID: 37924022 PMCID: PMC10625204 DOI: 10.1186/s12863-023-01165-y] [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] [Received: 02/23/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND As an important food and cash crop, identification of DNA molecular markers is of great significance for molecular marker-assisted breeding of Sorghum (Sorghum bicolor (L.) moench). Although some sorghum-related mutation databases have been published, the special SSR and SV databases still need to be constructed and updated. RESULTS In this study, the quality of 18 different sorghum genomes was evaluated, and two genomes were assembled at chromosome level. Through the identification and comparative analysis of SSR loci in these genomes, the distribution characteristics of SSR in the above sorghum genomes were initially revealed. At the same time, five representative reference genomes were selected to identify the structural variation of sorghum. Finally, a convenient SSR/SV database of sorghum was constructed by integrating the above results ( http://www.sorghum.top:8079/ ; http://43.154.129.150:8079/ ; http://47.106.184.91:8079/ ). Users can query the information of related sites and primer pairs. CONCLUSIONS Anyway, our research provides convenience for sorghum researchers and will play an active role in sorghum molecular marker-assisted breeding.
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Affiliation(s)
- Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Xiaobo Xia
- College of Plant Protection , Nanjing Agricultural University, Nanjing, 210095, China
| | - Huayan Zheng
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Shirui Yu
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China.
| | - Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, China.
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