Novel intron length polymorphic (ILP) markers from starch biosynthesis genes reveal genetic relationships in Indian wheat varieties and related species

Sharma, Himanshu; Bhandawat, Abhishek; Rahim, Mohammed Saba; Kumar, Pankaj; Choudhoury, Mohini Pal; Roy, Joy

doi:10.1007/s11033-020-05434-2

Cited by 17 publications

(13 citation statements)

References 36 publications

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“…The genetic classi cation of alliums (Fig- 2) allows us to identify speci c alliums to construct core collections (Birky1988). Using these molecular markers, various biotic and abiotic stress resistant genes might be introduced into premier cultivars of A.cepa.The characteristics of chloroplast genome such as lack of recombination and generally uniparental inheritance, makes chloroplast SSR markers suitable to understand plant evolution, population genetics, phylogeny, synteny, and domestication (Sharma et al 2020a).…”

Section: Scoring and Data Analysismentioning

confidence: 99%

Development of chloroplast derived SSR markers for genus Allium and their characterization in the allies for genetic improvement of alliums

Jayaswall

Sharma

Bhandawat

et al. 2022

Preprint

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Alliums are the most popular for their culinary usage and nutraceutical benefits. Their productions are greatly affected by the multiple biotic and abiotic stresses. Poor characterizations of genetic resources are the major bottleneck in genetic improvement of alliums. Chloroplast derived simple sequence repeat (cpSSR) have recently gained much popularity due to their maternal inheritance and low recombination along with their hypervariable nature. In this study, 22 chloroplast-derived SSR markers were produced from chloroplast genomes of A. cepa and A. sativum. Repeat comparison revealed tri nucleotide repeats were in higher proportion (50%) compared to other repeat motifs. The number of alleles ranged from 2 to 4, heterozygosity from 0.009 to 0.540, and PIC from 0.007 to 0.427. The polymorphism survey and clustering of twenty-two cpSSR markers of twenty-five alliums, lead to three groups (groups I, II, and III), indicated the usefulness of these cpSSR markers. This demonstrated that cultivated A. cepa and A. sativum belong to different groups II than most wild alliums, confirming the usefulness of the AccpSSR and AscpSSR markers that will allow introduction of desirable biotic and abiotic tolerance traits from various wild alliums to selected cultivated alliums. In addition, these cpSSRs were validated in 79 alliums, divided them into three groups using Jaccard dissimilarity and Bayesian model-based structure analysis. Subsequent clustering allowed us to identify diverse alliums, for constructing core collection of germplasm resource. The study will be useful for molecular breeding and genomic selection based crop improvement.

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Section: Scoring and Data Analysismentioning

confidence: 99%

Development of chloroplast derived SSR markers for genus Allium and their characterization in the allies for genetic improvement of alliums

Jayaswall

Sharma

Bhandawat

et al. 2022

Preprint

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“…These nuclear genome-derived markers, however, not conserved, are unable to identify maternally inherited relationships across cultivars, which is critical for understanding lineage and selection of multiple sources of resistance to different stresses. Furthermore, owing of their remarkable degree of sequence advancement, which prevents comparisons between sequences and allele sizes, the nuclear genome-based markers were less effective for identifying evolutionary relationships among alliums (Sharma et al 2020a;Sharma et al2020b). Chloroplast SSRs markers (cpSSRs) obtained from the chloroplast genome, on the other hand, have a number of advantages over nuclear genome-derived molecular markers, since these show maternal inheritance.…”

Section: Introductionmentioning

confidence: 99%

Development of chloroplast derived SSR markers for genus Allium and their characterization in the allies for genetic improvement of Alliums

Jayaswall,

Sharma,

Jayaswal

et al. 2023

South African Journal of Botany

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“…In eukaryotic genomes, there are generally some introns across each gene ( Hawkins, 1988 ; Deutsch and Long, 1999 ; Haas et al, 2005 ). Diversity of intron sequences between different individuals is abundant due to low selection pressure ( Stoltzfus et al, 1997 ; Panjabi et al, 2008 ; Sharma et al, 2020 ). Therefore, numerous intron polymorphism (IP) markers are available in the eukaryotic genome ( Badoni et al, 2016 ; Kita et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, numerous intron polymorphism (IP) markers are available in the eukaryotic genome ( Badoni et al, 2016 ; Kita et al, 2016 ). Studies have identified different types of IP, including ILP (Intron Length Polymorphism; Wang et al, 2005 ; Sharma et al, 2020 ) and ISNP (Intron Single Nucleotide Polymorphism; Ferreira et al, 2009 ; Liu et al, 2018 ). IP markers are generally co-dominant and highly polymorphic, and are widely used for constructing genetic maps, diversity analysis, and quantitative trait locus mapping ( Williams et al, 1990 ; Wei et al, 2005 ; Yang et al, 2007 ; Xia et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Development of Intron Polymorphism Markers and Their Association With Fatty Acid Component Variation in Oil Palm

Yang²,

Sun³

et al. 2022

Front. Plant Sci.

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Oil palm (Elaeis guineensis Jacq.) is a tropical woody oil crop of the palm family and is known as “the oil king of the world,” but its palm oil contains about 50% palmitic acid, which is considered unhealthy for humans. Intron polymorphisms (IP) are highly efficient and easily examined molecular markers located adjacent to exon regions of functional genes, thus may be associated with targeted trait variation. In order to speed up the breeding of oil palm fatty acid composition, the current study identified a total of 310 introns located within 52 candidate genes involved in fatty acid biosynthesis in the oil palm genome. Based on the intron sequences, 205 primer pairs were designed, 64 of which showed polymorphism among 70 oil palm individuals. Phenotypic variation of fatty acid content in the 70 oil palm individuals was also investigated. Association analysis revealed that 13 IP markers were significantly associated with fatty acid content variation, and these IP markers were located on chromosomes 2, 5, 6, 8, 9, and 10 of oil palm. The development of such IP markers may be useful for the genetic improvement of fatty acid composition in oil palm.

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Novel intron length polymorphic (ILP) markers from starch biosynthesis genes reveal genetic relationships in Indian wheat varieties and related species

Cited by 17 publications

References 36 publications

Development of chloroplast derived SSR markers for genus Allium and their characterization in the allies for genetic improvement of alliums

Development of chloroplast derived SSR markers for genus Allium and their characterization in the allies for genetic improvement of alliums

Development of chloroplast derived SSR markers for genus Allium and their characterization in the allies for genetic improvement of Alliums

Development of Intron Polymorphism Markers and Their Association With Fatty Acid Component Variation in Oil Palm

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