The Genome Sequence and Transcriptome Studies in Mango (Mangifera indica L.)

Singh, Nagendra; Mahato, Ajay Kumar; Jayaswal, Pawan Kumar

doi:10.1007/978-3-030-47829-2_10

Cited by 7 publications

(16 citation statements)

References 65 publications

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“…Apart from conventional breeding approaches, efforts have been made in the recent past to utilize biotechnological tools for marker-aided breeding. Significant progress has been made in the area of genome sequencing of mango by several researchers ( Singh et al., 2014 ; Luo et al., 2016 ; Singh et al., 2016 ; Kuhn et al., 2017 ; Wang et al., 2020 ). The wealth of genome resources has also been generated by our group as genome sequences of important mango cultivars (unpublished), and millions of SNPs have been identified, which has immense value in future mango breeding ( Singh et al., 2014 ; Mahato et al., 2016 ; Singh et al., 2016 ; Iquebal et al., 2017 ).…”

Section: Discussionmentioning

confidence: 99%

“…Few genetic maps in Mangifera indica have been constructed using different markers ( Kashkush et al., 2001 ; Singh et al., 2014 ; Luo et al., 2016 ; Singh et al., 2016 ; Kuhn et al., 2017 ; Wang et al., 2020 ). The integrated genetic linkage map reported here is of high density, as the number of markers is reasonably high.…”

Section: Discussionmentioning

confidence: 99%

“…However, the marker density across 20 LGs was relatively lower. In the current decade, a wealth of information on the mango genome has been generated ( Singh et al., 2014 ; Luo et al., 2016 ; Singh et al., 2016 ; Kuhn et al., 2017 ; Wang et al., 2020 ). This advancement in mango genomics has opened a new vista and may contribute to future mango improvement programs.…”

Section: Introductionmentioning

confidence: 99%

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High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids

Srivastav,

Radadiya,

Ramachandra

et al. 2023

Front. Plant Sci.

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IntroductionMango (Mangifera indica L.), acclaimed as the ‘king of fruits’ in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood.MethodsFor mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip array.Results and discussionInitially, we constructed two high-density linkage maps based on the segregation of female and male parents. A female map with 3,213 SNPs and male map with 1,781 SNPs were distributed on 20 linkages groups covering map lengths of 2,844.39 and 2,684.22cM, respectively. Finally, the integrated map was constructed comprised of 4,361 SNP markers distributed on 20 linkage groups, which consisted of the chromosome haploid number in Mangifera indica (n =20). The integrated genetic map covered the entire genome of Mangifera indica cv. Dashehari, with a total genetic distance of 2,982.75 cM and an average distance between markers of 0.68 cM. The length of LGs varied from 85.78 to 218.28 cM, with a mean size of 149.14 cM. Phenotyping for fruit color and firmness traits was done for two consecutive seasons. We identified important consistent QTLs for 12 out of 20 traits, with integrated genetic linkages having significant LOD scores in at least one season. Important consistent QTLs for fruit peel color are located at Chr 3 and 18, and firmness on Chr 11 and 20. The QTLs mapped in this study would be useful in the marker-assisted breeding of mango for improved efficiency.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids

Srivastav,

Radadiya,

Ramachandra

et al. 2023

Front. Plant Sci.

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“…The haploid genome size of M. indica is estimated to be 439 Mbp by flow cytometric analysis (Arumuganathan and Earle 1991). The first draft genome for M. indica was assembled for the Indian cultivar Amrapali (Singh et al 2014; Singh et al 2018). The genomes of M. indica cv.…”

Section: Introductionmentioning

confidence: 99%

Determination of phylogenetic relationships in the genusMangiferabased on whole chloroplast genome and nuclear genome sequences

Kumari Wijesundara,

Furtado,

Dillon

et al. 2023

Preprint

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The genus Mangifera (Anacardiaceae) includes 69 species of which Mangifera indica L. is the most important and primarily cultivated species for commercial mango production. Although the species are classified based on morphological descriptors, molecular evidence has proposed the hybrid origin of two species suggesting the possibility that more of the species may be of hybrid origin. To analyze evolutionary relationships within the genus, 13 samples representing 11 Mangifera species were sequenced and whole chloroplast (Cp) genomes and 47 common single-copy nuclear gene sequences were assembled and used for phylogenetic analysis using concatenation and coalescence-based methods. The Cp genome size varied from 151,752 to 158,965 bp with M. caesia and M. laurina having the smallest and largest genomes, respectively. Genome annotation revealed 80 protein-coding genes, 31 tRNA and four rRNA genes across all the species. Comparative analysis of whole Cp genome sequence and nuclear gene-based phylogenies revealed topological conflicts suggesting chloroplast capture or cross hybridization. The Cp genomes of M. altissima, M. applanata, M. caloneura and M. lalijiwa were similar to those of M. indica (99.9% sequence similarity). Their close sequence relationship suggests a common ancestry and likely cross-hybridization between wild relatives and M. indica. This study provides improved knowledge of phylogenetic relationships in Mangifera, indicating extensive gene flow among the different species, suggesting that hybrids may be common within the genus.

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“…First, the Indian cultivar 'Amrapali' was assembled with Illumina reads. The large assembly size (492Mbp) achieved compared to the estimated genome size (439Mbp) indicated the redundancy in the assembly [19]. In 2020, cultivar 'Alphonso' was assembled using PacBio long reads, Illumina, and Hi-C reads leading to an improved 392Mb genome [20].…”

mentioning

confidence: 99%

A telomere-to-telomere genome of mango exclusively from long-read sequence data

Henry,

Wijesundara,

Furtado

et al. 2023

Preprint

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Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin mapping (Hi-C). We report here a telomere-to-telomere chromosome-level mango genome using only PacBio HiFi long reads. HiFi reads at high coverage (204X) resulted in the assembly of 17 chromosomes each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs with telomeres at one end and ribosomal repeats at the other end. Analysing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere. The assembled genome was 365 Mb with 100% completeness as assessed by BUSCO analysis. The haplotypes assembled demonstrated extensive structural differences. This approach may be useful for assembling telomere-to-telomere and haplotype-resolved genomes for many other plants.

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The Genome Sequence and Transcriptome Studies in Mango (Mangifera indica L.)

Cited by 7 publications

References 65 publications

High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids

High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids

Determination of phylogenetic relationships in the genusMangiferabased on whole chloroplast genome and nuclear genome sequences

A telomere-to-telomere genome of mango exclusively from long-read sequence data

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