A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits
Abstract Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronom...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-03-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20175 |
| _version_ | 1819159698744541184 |
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| author | Thomas H. Pendergast, IV Peng Qi Damaris Achieng Odeny Mathews M. Dida Katrien M. Devos |
| author_facet | Thomas H. Pendergast, IV Peng Qi Damaris Achieng Odeny Mathews M. Dida Katrien M. Devos |
| author_sort | Thomas H. Pendergast, IV |
| collection | DOAJ |
| description | Abstract Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F2:3 population in a Kenyan field trial. The F2:3 population was genotyped via genotyping‐by‐sequencing (GBS) and the UGbS‐Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18‐linkage‐group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE‐RICH REPEAT‐CONTAINING PROTEIN genes, with homology to nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high‐marker‐density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance. |
| first_indexed | 2024-12-22T16:44:42Z |
| format | Article |
| id | doaj.art-2a130197883d41d29d2ca818a95aacdc |
| institution | Directory Open Access Journal |
| issn | 1940-3372 |
| language | English |
| last_indexed | 2024-12-22T16:44:42Z |
| publishDate | 2022-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj.art-2a130197883d41d29d2ca818a95aacdc2022-12-21T18:19:45ZengWileyThe Plant Genome1940-33722022-03-01151n/an/a10.1002/tpg2.20175A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traitsThomas H. Pendergast, IV0Peng Qi1Damaris Achieng Odeny2Mathews M. Dida3Katrien M. Devos4Dep. of Plant Biology Univ. of Georgia Athens GA 30602 USADep. of Plant Biology Univ. of Georgia Athens GA 30602 USAThe International Crops Research Institute for the Semi‐Arid Tropics–Eastern and Southern Africa Nairobi KenyaDep. of Applied Sciences Maseno Univ. Private Bag‐40105 Maseno KenyaDep. of Plant Biology Univ. of Georgia Athens GA 30602 USAAbstract Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F2:3 population in a Kenyan field trial. The F2:3 population was genotyped via genotyping‐by‐sequencing (GBS) and the UGbS‐Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18‐linkage‐group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE‐RICH REPEAT‐CONTAINING PROTEIN genes, with homology to nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high‐marker‐density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.https://doi.org/10.1002/tpg2.20175 |
| spellingShingle | Thomas H. Pendergast, IV Peng Qi Damaris Achieng Odeny Mathews M. Dida Katrien M. Devos A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits The Plant Genome |
| title | A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits |
| title_full | A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits |
| title_fullStr | A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits |
| title_full_unstemmed | A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits |
| title_short | A high‐density linkage map of finger millet provides QTL for blast resistance and other agronomic traits |
| title_sort | high density linkage map of finger millet provides qtl for blast resistance and other agronomic traits |
| url | https://doi.org/10.1002/tpg2.20175 |
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