Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding
Guava (Psidium guajava L.), a rich source of nutrients, is an important tropical and subtropical fruit of the Myrtaceae family and exhibits magnificent diversity. Genetic diversity analysis is the first step toward the identification of parents for hybridization, genetic mapping, and molecular breed...
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doaj-551f3bc71a8a459bab76e6a8ded1f5992021-09-23T04:22:34ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-09-011210.3389/fpls.2021.708332708332Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular BreedingSujata Thakur0Inderjit Singh Yadav1Manish Jindal2Parva Kumar Sharma3Guriqbal Singh Dhillon4Rajbir Singh Boora5Naresh Kumar Arora6Manav Indra Singh Gill7Parveen Chhuneja8Amandeep Mittal9School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaSchool of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaSchool of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaSchool of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaSchool of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaFruit Research Sub-Station, Punjab Agricultural University, Bahadurgarh, IndiaDepartment of Fruit Science, Punjab Agricultural University, Ludhiana, IndiaDepartment of Fruit Science, Punjab Agricultural University, Ludhiana, IndiaSchool of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaSchool of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaGuava (Psidium guajava L.), a rich source of nutrients, is an important tropical and subtropical fruit of the Myrtaceae family and exhibits magnificent diversity. Genetic diversity analysis is the first step toward the identification of parents for hybridization, genetic mapping, and molecular breeding in any crop species. A diversity analysis based on whole-genome functional markers increases the chances of identifying genetic associations with agronomically important traits. Therefore, here, we sequenced the genome of guava cv. Allahabad Safeda on an Illumina platform and generated a draft assembly of ~304 MB. The assembly of the Allahabad Safeda genome constituted >37.95% repeat sequences, gene prediction with RNA-seq data as evidence identified 14,115 genes, and BLAST n/r, Interproscan, PfamScan, BLAST2GO, and KEGG annotated 13,957 genes. A comparative protein transcript analysis of tree species revealed the close relatedness of guava with Eucalyptus. Comparative transcriptomics-based SSR/InDel/SNP-PCR ready genome-wide markers in greenish-yellow skinned and white fleshed-Allahabad Safeda to four contrasting cultivars viz apple-color-skinned and white-fleshed-Lalima, greenish-yellow-skinned and pink-fleshed-Punjab Pink, purple-black-skinned and purple-fleshed-Purple Local and widely used rootstock-Lucknow-49 were developed. The molecular markers developed here revealed a high level of individual heterozygosity within genotypes in 22 phenotypically diverse guava cultivars. Principal coordinate, STRUCTURE clustering, and neighbor-joining-based genetic diversity analysis identified distinct clusters associated with fruit skin and flesh color. The genome sequencing of guava, functional annotation, comparative transcriptomics-based genome-wide markers, and genetic diversity analysis will expand the knowledge of genomes of climacteric fruits, facilitating trait-based molecular breeding and diversifying the nutritional basket.https://www.frontiersin.org/articles/10.3389/fpls.2021.708332/fullPsidium guajava L.Allahabad Safedagenome assemblygene prediction and annotationcomparative transcriptomicsfunctional markers |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Sujata Thakur Inderjit Singh Yadav Manish Jindal Parva Kumar Sharma Guriqbal Singh Dhillon Rajbir Singh Boora Naresh Kumar Arora Manav Indra Singh Gill Parveen Chhuneja Amandeep Mittal |
spellingShingle |
Sujata Thakur Inderjit Singh Yadav Manish Jindal Parva Kumar Sharma Guriqbal Singh Dhillon Rajbir Singh Boora Naresh Kumar Arora Manav Indra Singh Gill Parveen Chhuneja Amandeep Mittal Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding Frontiers in Plant Science Psidium guajava L. Allahabad Safeda genome assembly gene prediction and annotation comparative transcriptomics functional markers |
author_facet |
Sujata Thakur Inderjit Singh Yadav Manish Jindal Parva Kumar Sharma Guriqbal Singh Dhillon Rajbir Singh Boora Naresh Kumar Arora Manav Indra Singh Gill Parveen Chhuneja Amandeep Mittal |
author_sort |
Sujata Thakur |
title |
Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding |
title_short |
Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding |
title_full |
Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding |
title_fullStr |
Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding |
title_full_unstemmed |
Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding |
title_sort |
development of genome-wide functional markers using draft genome assembly of guava (psidium guajava l.) cv. allahabad safeda to expedite molecular breeding |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2021-09-01 |
description |
Guava (Psidium guajava L.), a rich source of nutrients, is an important tropical and subtropical fruit of the Myrtaceae family and exhibits magnificent diversity. Genetic diversity analysis is the first step toward the identification of parents for hybridization, genetic mapping, and molecular breeding in any crop species. A diversity analysis based on whole-genome functional markers increases the chances of identifying genetic associations with agronomically important traits. Therefore, here, we sequenced the genome of guava cv. Allahabad Safeda on an Illumina platform and generated a draft assembly of ~304 MB. The assembly of the Allahabad Safeda genome constituted >37.95% repeat sequences, gene prediction with RNA-seq data as evidence identified 14,115 genes, and BLAST n/r, Interproscan, PfamScan, BLAST2GO, and KEGG annotated 13,957 genes. A comparative protein transcript analysis of tree species revealed the close relatedness of guava with Eucalyptus. Comparative transcriptomics-based SSR/InDel/SNP-PCR ready genome-wide markers in greenish-yellow skinned and white fleshed-Allahabad Safeda to four contrasting cultivars viz apple-color-skinned and white-fleshed-Lalima, greenish-yellow-skinned and pink-fleshed-Punjab Pink, purple-black-skinned and purple-fleshed-Purple Local and widely used rootstock-Lucknow-49 were developed. The molecular markers developed here revealed a high level of individual heterozygosity within genotypes in 22 phenotypically diverse guava cultivars. Principal coordinate, STRUCTURE clustering, and neighbor-joining-based genetic diversity analysis identified distinct clusters associated with fruit skin and flesh color. The genome sequencing of guava, functional annotation, comparative transcriptomics-based genome-wide markers, and genetic diversity analysis will expand the knowledge of genomes of climacteric fruits, facilitating trait-based molecular breeding and diversifying the nutritional basket. |
topic |
Psidium guajava L. Allahabad Safeda genome assembly gene prediction and annotation comparative transcriptomics functional markers |
url |
https://www.frontiersin.org/articles/10.3389/fpls.2021.708332/full |
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