A novel SNP panel developed for targeted genotyping-by-sequencing (GBS) reveals genetic diversity and population structure of Musa spp. germplasm collection

Gardoce, Roanne R.; Manohar, Anand Noel C.; Mendoza, Jay-Vee S.; Tejano, Maila S.; Nocum, Jen Daine L.; Lachica, Grace C.; Gueco, Lavernee S.; Cueva, Fe M. Dela; Lantican, Darlon V.

doi:10.1007/s00438-023-02018-0

Cited by 4 publications

(4 citation statements)

References 34 publications

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“…Furthermore, due to the high complexity of the Musa genome composition and ploidy levels, the observed heterozygosity (Ho) for all six DNA markers ranges from 0.49 to 0.94, which is greater than the expected heterozygosity (He: 0.39-0.53). As a result, the population’s fixation index or inbreeding coefficient (FIS) was negative for all markers indicating high or excess heterozygosity (Meisner and Albrechtsen 2019) in the sampled natural population which is consistent with the findings of Gardoce et al (2023). The polymorphism information content (PIC) for all markers ranges from 0.31 ( CKL AS-PCR marker) to 0.49 ( RLCK-VI SSR marker).…”

Section: Resultssupporting

confidence: 83%

“…The formation of two major groups within the wild M. balbisiana accessions is due to its intra-population genetic diversity. Interestingly, one accession of M. textilis ('Abaca') formed a group with the wild M. balbisiana accessions coinciding with the results of Gardoce et al (2023). Nonetheless, hybrid bananas with varying ploidy levels also established a significant cluster (IV) due to heterozygosity scores, regardless of their A or B-genome dosage, in the target alleles.…”

Section: Genetic Diversitymentioning

confidence: 54%

“…Ten banana accessions representing different major banana genomic groups were carefully selected from the 183 banana accessions in the ex situ germplasm collection of the National Plant Genetic Resources Laboratory at the Institute of Plant Breeding (NPGRL-IPB)-UPLB utilized in the study of Gardoce et al (2023). These accessions were utilized as plant materials to perform partial gene sequencing of putative RLKs as the basis for identification of potential polymorphic regions as target for DNA marker development (Table 1).…”

Section: Methodsmentioning

confidence: 99%

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Development and validation of allele specificRLKgene markers for banana bunchy top disease (BBTD) resistance in banana

Caro,

Manohar,

Gardoce

et al. 2023

Preprint

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As global demand for bananas rises, the threat of banana bunchy top disease (BBTD), caused bybanana bunchy top virus(BBTV), poses a significant constraint to sustainable banana production. To circumvent this, it is critical to fast-track the development of BBTV-resistant banana cultivars. In a dataset of differentially expressed genes between BBTV-resistant and susceptible bananas, sixRLKgenes involved in plant defense against pathogens were exclusively upregulated in the BBTV-resistant wildMusa balbisianacompared to the BBTV-susceptibleMusa acuminatacv. ’Lakatan’. Here, two genic variants ofRLKs, single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSR), were identified in 10 banana accessions representing major genomic groupings. Nine gene-specific markers were developed using three marker systems: SSR, allele-specific PCR, and tetra primer amplification refractory mutation system PCR markers. Six of these were polymorphic and successfully discriminated 117Musagenotypes at the NPGRL-IPBex situgermplasm, with an average polymorphism information content of 0.36 for SNP markers and 0.49 for SSR marker, both of which are moderately informative. These markers facilitated the construction of a dendrogram using the Unweighted Neighbor-Joining (UNJ) method with 1000 bootstrap iterations, identifying four major clades:M. acuminataspp. and otherMusaspp. (I), wildM. balbisiana(BBw) and other accessions with high-proportion of B-genome (II & III), hybrid bananas (triploids and tetraploids) (IV), which revealed the genetic diversity and relationships amongMusaaccessions. Ultimately, this genomic resource will aid in positioning the Philippines as a key player in banana disease resistance breeding towards a food-secure banana industry.

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Section: Resultssupporting

confidence: 83%

Section: Genetic Diversitymentioning

confidence: 54%

Section: Methodsmentioning

confidence: 99%

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Development and validation of allele specificRLKgene markers for banana bunchy top disease (BBTD) resistance in banana

Caro,

Manohar,

Gardoce

et al. 2023

Preprint

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“…Alberto [14] used SNP markers in DNA sequencing data related to restriction enzyme sites to study and compare the chromosome structures of 36 banana varieties belonging to the ABB genotype (including different subspecies). Gardoce [16] developed a 1 K SNP genotyping panel, effectively distinguishing between genomic groups, based on the filtering of high-quality genomewide SNPs from the Musa Germplasm Information System, and used it to assess the genetic diversity and population structure of 183 Musa spp. accessions.…”

Section: Introductionmentioning

confidence: 99%

Banana Classification Using Sanger Sequencing of the Ribosomal DNA Internal Transcribed Spacers (ITS)

Zeng,

Huang,

et al. 2024

Preprint

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Many types of banana (Musa spp.)—one of the most economically important horticultural crops—exist, and their ploidy (diploid, triploid, and tetraploid, usually) and genome types (containing A or/and B genome in most cases) differ. At present, observation and genome type detection are commonly used to identify banana germplasm resources. However, the former is tedious, while the latter cannot distinguish categories below genome types. It is therefore urgent that a simple and effective method for identifying banana germplasm resources is established. We sequenced and analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 62 banana germplasm and found that the sequencing peaks, especially the 20 bp region near the 420 bp position (referred to as the “420 bp region”), exhibited relatively recognizable and repeatable polymorphism characteristics. Using the “420 bp region” as a marker, we were able to quickly distinguish bananas belonging to different genome type groups (comprising the AA, AB, AAA, ABB, AAB, ABBB, AAAB, and AAAA groups) or different subgroups in the same genome type group (for example, the Cavendish, Gros Michel, Red, Lakatan, and Ibota Bota subgroups in the AAA group; and the Pisang Raja, Plantain, Pome and Silk subgroups in the AAB group). Moreover, it appeared that Sanger sequencing of ITS could be used for identifying banana hybrid offspring. These results demonstrated that the banana ITS region contains rich genetic information that is useful for genotyping. In general, ITS sequencing simplifies the classification of banana germplasm resources and has potential application in several areas of Musa improvement.

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Development of allele-specific RLK gene markers towards banana bunchy top disease resistance and germplasm management

Caro,

Manohar,

Gardoce

et al. 2024

Physiological and Molecular Plant Pathology

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A novel SNP panel developed for targeted genotyping-by-sequencing (GBS) reveals genetic diversity and population structure of Musa spp. germplasm collection

Cited by 4 publications

References 34 publications

Development and validation of allele specificRLKgene markers for banana bunchy top disease (BBTD) resistance in banana

Development and validation of allele specificRLKgene markers for banana bunchy top disease (BBTD) resistance in banana

Banana Classification Using Sanger Sequencing of the Ribosomal DNA Internal Transcribed Spacers (ITS)

Development of allele-specific RLK gene markers towards banana bunchy top disease resistance and germplasm management

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