RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (<i>Musa textilis</i> Nee)
Despite the importance of and current demand for abaca (<i>Musa textilis</i> Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tan...
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| Format: | Article |
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MDPI AG
2022-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/3/519 |
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| author | Nelzo C. Ereful Antonio G. Lalusin Antonio C. Laurena |
| author_facet | Nelzo C. Ereful Antonio G. Lalusin Antonio C. Laurena |
| author_sort | Nelzo C. Ereful |
| collection | DOAJ |
| description | Despite the importance of and current demand for abaca (<i>Musa textilis</i> Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tangongon), one wild banana variety (<i>Musa balbisiana</i> Colla) Pacol, and two developed backcrosses (Abuab × Pacol BC<sub>2</sub> and BC<sub>3</sub>) were grown at the Institute of Plant Breeding (IPB), Laguna, Philippines. The pseudostems of 3-month-old suckers of each genotype were sampled for RNA-seq. Datasets were analyzed for differential expression (DE) implementing various model frameworks, including pairwise, genotypic and non-DE models. Results indicate that Abuab and BC<sub>3</sub> induce the highest proportion (70%) of abaca-specific genes. Gene ontology (GO) enrichment analysis showed several genes associated with cellulose synthase activity, callose synthase, ß-glucosidase activity, glucan biosynthetic process, etc. KEGG pathway analysis showed several genes encoding for enzymes involved in the lignin biosynthetic pathway. Analysis using genotypic DE (GDE) between abaca bunchy top virus (AbBTV)-resistant and -susceptible groups revealed genes such as pathogenesis-related protein and NBS-LRR. As the genotypes were not infected with the pathogen, these genes are yet to be confirmed for their roles in disease resistance and are an interesting subject for further investigation. |
| first_indexed | 2024-03-09T19:47:52Z |
| format | Article |
| id | doaj.art-ffbff8719e6e496aac82eacb806d5e03 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T19:47:52Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-ffbff8719e6e496aac82eacb806d5e032023-11-24T01:19:29ZengMDPI AGGenes2073-44252022-03-0113351910.3390/genes13030519RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (<i>Musa textilis</i> Nee)Nelzo C. Ereful0Antonio G. Lalusin1Antonio C. Laurena2Philippine Genome Center for Agriculture, University of the Philippines Los Baños, Laguna 4031, PhilippinesInstitute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, PhilippinesPhilippine Genome Center for Agriculture, University of the Philippines Los Baños, Laguna 4031, PhilippinesDespite the importance of and current demand for abaca (<i>Musa textilis</i> Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tangongon), one wild banana variety (<i>Musa balbisiana</i> Colla) Pacol, and two developed backcrosses (Abuab × Pacol BC<sub>2</sub> and BC<sub>3</sub>) were grown at the Institute of Plant Breeding (IPB), Laguna, Philippines. The pseudostems of 3-month-old suckers of each genotype were sampled for RNA-seq. Datasets were analyzed for differential expression (DE) implementing various model frameworks, including pairwise, genotypic and non-DE models. Results indicate that Abuab and BC<sub>3</sub> induce the highest proportion (70%) of abaca-specific genes. Gene ontology (GO) enrichment analysis showed several genes associated with cellulose synthase activity, callose synthase, ß-glucosidase activity, glucan biosynthetic process, etc. KEGG pathway analysis showed several genes encoding for enzymes involved in the lignin biosynthetic pathway. Analysis using genotypic DE (GDE) between abaca bunchy top virus (AbBTV)-resistant and -susceptible groups revealed genes such as pathogenesis-related protein and NBS-LRR. As the genotypes were not infected with the pathogen, these genes are yet to be confirmed for their roles in disease resistance and are an interesting subject for further investigation.https://www.mdpi.com/2073-4425/13/3/519abacaRNA-seqdifferential expressionfiber qualityabaca bunchy top virus |
| spellingShingle | Nelzo C. Ereful Antonio G. Lalusin Antonio C. Laurena RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (<i>Musa textilis</i> Nee) Genes abaca RNA-seq differential expression fiber quality abaca bunchy top virus |
| title | RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (<i>Musa textilis</i> Nee) |
| title_full | RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (<i>Musa textilis</i> Nee) |
| title_fullStr | RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (<i>Musa textilis</i> Nee) |
| title_full_unstemmed | RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (<i>Musa textilis</i> Nee) |
| title_short | RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (<i>Musa textilis</i> Nee) |
| title_sort | rna seq reveals differentially expressed genes associated with high fiber quality in abaca i musa textilis i nee |
| topic | abaca RNA-seq differential expression fiber quality abaca bunchy top virus |
| url | https://www.mdpi.com/2073-4425/13/3/519 |
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