Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.)
Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the devastating disease affecting common bean production and productivity worldwide. Several quantitative trait loci (QTLs) for anthracnose resistance have been identified. In order to make use of these QTLs in common bean br...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.966339/full |
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| author | Safoora Shafi Dinesh Kumar Saini Mohd Anwar Khan Vanya Bawa Neeraj Choudhary Waseem Ali Dar Arun K. Pandey Rajeev Kumar Varshney Reyazul Rouf Mir |
| author_facet | Safoora Shafi Dinesh Kumar Saini Mohd Anwar Khan Vanya Bawa Neeraj Choudhary Waseem Ali Dar Arun K. Pandey Rajeev Kumar Varshney Reyazul Rouf Mir |
| author_sort | Safoora Shafi |
| collection | DOAJ |
| description | Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the devastating disease affecting common bean production and productivity worldwide. Several quantitative trait loci (QTLs) for anthracnose resistance have been identified. In order to make use of these QTLs in common bean breeding programs, a detailed meta-QTL (MQTL) analysis has been conducted. For the MQTL analysis, 92 QTLs related to anthracnose disease reported in 18 different earlier studies involving 16 mapping populations were compiled and projected on to the consensus map. This meta-analysis led to the identification of 11 MQTLs (each involving QTLs from at least two different studies) on 06 bean chromosomes and 10 QTL hotspots each involving multiple QTLs from an individual study on 07 chromosomes. The confidence interval (CI) of the identified MQTLs was found 3.51 times lower than the CI of initial QTLs. Marker-trait associations (MTAs) reported in published genome-wide association studies (GWAS) were used to validate nine of the 11 identified MQTLs, with MQTL4.1 overlapping with as many as 40 MTAs. Functional annotation of the 11 MQTL regions revealed 1,251 genes including several R genes (such as those encoding for NBS-LRR domain-containing proteins, protein kinases, etc.) and other defense related genes. The MQTLs, QTL hotspots and the potential candidate genes identified during the present study will prove useful in common bean marker-assisted breeding programs and in basic studies involving fine mapping and cloning of genomic regions associated with anthracnose resistance in common beans. |
| first_indexed | 2024-04-14T02:43:10Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-14T02:43:10Z |
| publishDate | 2022-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-29b3bd4bab164efca41bc2fbc8d3cd582022-12-22T02:16:44ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-08-011310.3389/fpls.2022.966339966339Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.)Safoora Shafi0Dinesh Kumar Saini1Mohd Anwar Khan2Vanya Bawa3Neeraj Choudhary4Waseem Ali Dar5Arun K. Pandey6Rajeev Kumar Varshney7Reyazul Rouf Mir8Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, IndiaDepartment of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, IndiaDivision of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, IndiaDivision of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Jammu, Chatha, Jammu and Kashmir, IndiaDivision of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST-Jammu, Chatha, Jammu and Kashmir, IndiaMountain Agriculture Research and Extension Station, SKUAST-Kashmir, Bandipora, Jammu and Kashmir, IndiaCollege of Life Sciences, China Jiliang University, Hangzhou, ChinaState Agricultural Biotechnology Centre, Centre for Crop & Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, AustraliaDivision of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, Wadura, IndiaAnthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the devastating disease affecting common bean production and productivity worldwide. Several quantitative trait loci (QTLs) for anthracnose resistance have been identified. In order to make use of these QTLs in common bean breeding programs, a detailed meta-QTL (MQTL) analysis has been conducted. For the MQTL analysis, 92 QTLs related to anthracnose disease reported in 18 different earlier studies involving 16 mapping populations were compiled and projected on to the consensus map. This meta-analysis led to the identification of 11 MQTLs (each involving QTLs from at least two different studies) on 06 bean chromosomes and 10 QTL hotspots each involving multiple QTLs from an individual study on 07 chromosomes. The confidence interval (CI) of the identified MQTLs was found 3.51 times lower than the CI of initial QTLs. Marker-trait associations (MTAs) reported in published genome-wide association studies (GWAS) were used to validate nine of the 11 identified MQTLs, with MQTL4.1 overlapping with as many as 40 MTAs. Functional annotation of the 11 MQTL regions revealed 1,251 genes including several R genes (such as those encoding for NBS-LRR domain-containing proteins, protein kinases, etc.) and other defense related genes. The MQTLs, QTL hotspots and the potential candidate genes identified during the present study will prove useful in common bean marker-assisted breeding programs and in basic studies involving fine mapping and cloning of genomic regions associated with anthracnose resistance in common beans.https://www.frontiersin.org/articles/10.3389/fpls.2022.966339/fullcommon beansanthracnoseQTLmeta-QTLGWAScandidate genes |
| spellingShingle | Safoora Shafi Dinesh Kumar Saini Mohd Anwar Khan Vanya Bawa Neeraj Choudhary Waseem Ali Dar Arun K. Pandey Rajeev Kumar Varshney Reyazul Rouf Mir Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.) Frontiers in Plant Science common beans anthracnose QTL meta-QTL GWAS candidate genes |
| title | Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.) |
| title_full | Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.) |
| title_fullStr | Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.) |
| title_full_unstemmed | Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.) |
| title_short | Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.) |
| title_sort | delineating meta quantitative trait loci for anthracnose resistance in common bean phaseolus vulgaris l |
| topic | common beans anthracnose QTL meta-QTL GWAS candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.966339/full |
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