Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (Juglans regia L.)
In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for...
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| creator | Itoo, H. Shah, Rafiq Ahmad Qurat, S. Jeelani, Afnan Khursheed, Sheikh Bhat, Zahoor A. Mir, M. A. Rather, G. H. Zargar, Sajad Majeed Shah, M. D. Padder, Bilal A. |
| description | In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection. |
| doi_str_mv | 10.1007/s13205-023-03563-6 |
| format | Article |
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The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection.</description><identifier>ISSN: 2190-572X</identifier><identifier>ISSN: 2190-5738</identifier><identifier>EISSN: 2190-5738</identifier><identifier>DOI: 10.1007/s13205-023-03563-6</identifier><identifier>PMID: 37124992</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Agriculture ; Bioinformatics ; Biomaterials ; Biotechnology ; Cancer Research ; Chemistry ; Chemistry and Materials Science ; chromosome mapping ; Gene mapping ; Genetic analysis ; Genetic diversity ; genetic variation ; genome ; Genomes ; genotype ; Genotypes ; heat ; Himalayan region ; Juglans regia ; Marker-assisted selection ; Original ; Original Article ; Population genetics ; Population structure ; Quantitative trait loci ; Repositories ; Stem Cells ; variance ; Variance analysis ; Walnuts</subject><ispartof>3 Biotech, 2023-05, Vol.13 (5), p.136-136, Article 136</ispartof><rights>King Abdulaziz City for Science and Technology 2023. 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D.</au><au>Padder, Bilal A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (Juglans regia L.)</atitle><jtitle>3 Biotech</jtitle><stitle>3 Biotech</stitle><addtitle>3 Biotech</addtitle><date>2023-05-01</date><risdate>2023</risdate><volume>13</volume><issue>5</issue><spage>136</spage><epage>136</epage><pages>136-136</pages><artnum>136</artnum><issn>2190-572X</issn><issn>2190-5738</issn><eissn>2190-5738</eissn><abstract>In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. 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| subjects | Agriculture Bioinformatics Biomaterials Biotechnology Cancer Research Chemistry Chemistry and Materials Science chromosome mapping Gene mapping Genetic analysis Genetic diversity genetic variation genome Genomes genotype Genotypes heat Himalayan region Juglans regia Marker-assisted selection Original Original Article Population genetics Population structure Quantitative trait loci Repositories Stem Cells variance Variance analysis Walnuts |
| title | Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (Juglans regia L.) |
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