Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz)

Udoh, Lovina I.; Gedil, Melaku; Parkes, Elizabeth; Kulakow, Peter; Adesoye, Adenubi; Nwuba, Chiamaka; Rabbi, Ismail

doi:10.1007/s11032-017-0718-5

Cited by 16 publications

(20 citation statements)

References 40 publications

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“…DNA mutations like single nucleotide polymorphisms (SNPs) and insertion/deletions (InDels) are associated with the phenotypic diversity of crop plants (Vignesh et al 2013;Saini et al 2016;Udoh et al 2017). The function of gene is altered when SNPs or InDels present in the coding region of gene causes change in the amino acid sequence and such nucleotide changes are called "functional nucleotide polymorphisms (FNPs)".…”

Section: Introductionmentioning

confidence: 99%

“…In both crtRB1 and lcyE, transposon had played a major role for creation of different alleles with diverse function (Harjes et al 2008;Yan et al 2010). Sequencing of alleles of candidate genes and subsequent discovery of FNPs would be useful in the development of functional markers for precise and accurate genotyping in marker-assisted breeding program (Saini et al 2016;Udoh et al 2017). Through sequence analysis of 3′ UTR of crtRB1 gene, Vignesh et al (2013) discovered SNP4, SNP13, InDel6 and InDel7 as functional variations that clearly discriminated the high and the low β-carotene genotypes belonging to Indian and exotic origin.…”

Section: Introductionmentioning

confidence: 99%

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Molecular characterization of 5′ UTR of the lycopene epsilon cyclase (lcyE) gene among exotic and indigenous inbreds for its utilization in maize biofortification

et al. 2018

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Maize grains are the important source of food and energy, but possess very low proA (< 2.5 µg/g) compared to target level of 15 µg/g set by HarvestPlus to alleviate VAD. Favorable allele having variation in 5' untranslated region (UTR) of () gene enhances concentration of proA in maize. To identify the sequence variation in 5' UTR of , a set of diverse 13 inbreds of indigenous and exotic origin was characterized for allelic constitution of. Inbreds possessed wide variation in proA (1.62-23.12 µg/g) with a mean of 9.64 µg/g. The proA in CIMMYT-HarvestPlus genotypes having favorable allele of was very high (22.28 µg/g), whereas the Indian inbreds with the same allele possessed very low proA (2.48 µg/g). Eight genotypes viz., HKI161, HKI163, HKI161-PV, HKI163-PV, HKI193-1-PV, HKI193-2-PV, HP704-22 and HP704-23 revealed the presence of favorable allele, while VQL1, DMRIL47, MGU-PV-123/C6, HKI193-1 and HKI193-2 showed the presence of unfavorable allele of gene. Sequence comparison of favorable allele of Indian (HKI161 and HKI163) and exotic genotypes (HP704-22 and HP704-23) revealed seven having three transitions ( and : G to A,: C to T) and four transversions (: C to G, : T to G,: G to C and : G to T). Four (: position 446, : position 458,: position 459 and : position 483) discriminated the low- and high- proA lines having favorable allele of. These hold significance in enrichment of proA in maize for marker development and their use in marker-assisted selection.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular characterization of 5′ UTR of the lycopene epsilon cyclase (lcyE) gene among exotic and indigenous inbreds for its utilization in maize biofortification

et al. 2018

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“…The latter finding is consistent with previous work in which knocking out the MdDIPM4 gene via CRISPR/Cas9 led to a 50% reduction in fire blight symptoms on notoriously susceptible 'Gala' and 'Golden Delicious' cultivars 40 . These results also highlight utilization of candidate-gene based association studies to rapidly identify molecular markers linked to traits of interest for progeny and parent selection in breeding programs 59 . Breeding from a perspective of susceptibility rather than resistance can help resolve issues in tree fruit crops where linkage drag and cross incompatibility between Malus species and cultivated apples makes introgression of resistance alleles not feasible or very time consuming in many cases 11 .…”

Section: Discussionmentioning

confidence: 87%

Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm

Tegtmeier

Pompili

Singh

et al. 2020

Sci Rep

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Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in fire blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p < 0.05) with fire blight susceptibility traits, while two of these SNPs showed highly significant (p < 0.001) associations across two different years. This research has provided knowledge about genetic diversity in fire blight S genes in diverse apple accessions and identified candidate HIPM and DIPM alleles that could be used to develop apple cultivars with decreased fire blight susceptibility via marker-assisted breeding or biotechnological approaches.

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“…Another study by Khanal et al [61] employed KASP SNPs to determine the genetic variability present in 26 isolates of Rotylenchulus reniformis a plant parasitic nematode of cotton and soybean, this will be of benefit in resistant breeding programs. Also, Udoh et al [62] developed KASP SNP markers for phytoene synthase2 gene associated with carotenoids in cassava. The validation SNP makers explained most of the proportion of phenotypic variation for carotenoids in a genetic gain cassava population.…”

Section: Resultsmentioning

confidence: 99%

Single Nucleotide Polymorphisms: A Modern Tool to Screen Plants for Desirable Traits

Udoh¹,

Obaseojei²,

Uzoebo³

2021

Plant Breeding - Current and Future Views

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Single nucleotide polymorphism (SNP) represent a change in a single nucleotide within the genome. This can alter the phenotype of an individual within the same species if it occurs in a coding region of the gene. The change in nucleotide can produce desirable characteristic in plants and can become an object for selection. New SNPs have been discovered and subsequently converted to molecular markers using various non-gel based and next generation sequencing platforms. Considering that SNP markers are based on target genes, its abundance in the genome, high automation and multiplexability, has made it a marker of choice and an effective tool for screening plant germplasm for desirable traits. This chapter considers SNP as molecular marker, their discovery and different SNP genotyping methods was documented. A few case studies of SNP as allele specific markers and their association with traits of interest was considered. Thus, highlighting their efficacy as useful tool for marker assisted selection and plant germplasms screening.

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Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz)

Cited by 16 publications

References 40 publications

Molecular characterization of 5′ UTR of the lycopene epsilon cyclase (lcyE) gene among exotic and indigenous inbreds for its utilization in maize biofortification

Molecular characterization of 5′ UTR of the lycopene epsilon cyclase (lcyE) gene among exotic and indigenous inbreds for its utilization in maize biofortification

Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm

Single Nucleotide Polymorphisms: A Modern Tool to Screen Plants for Desirable Traits

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