Dissecting the plant genome: through new generation molecular markers

Choudhury, Amrita Roy; Deb, Sohini; Kharbyngar, Banridor; Rajpal, Vijay Rani; Rao, Satyawada Rama

doi:10.1007/s10722-022-01441-3

Cited by 16 publications

(4 citation statements)

References 113 publications

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“…Detailed agro-morphological characterization and assessment of patterns of genetic variability based on quantitative and qualitative traits is the rst and crucial step in describing available genetic resources and their e cient use in breeding programs (Balkaya and Yanmaz 2005;Oumata et al 2023). However, although agro-morphological traits can be controlled at the genetic level, they may be nonspeci c and non-polymorphic, and their variation could be strongly in uenced by environmental factors (Choudhury et al 2022;Petit et al 2020;Terlević et al 2023). In contrast, DNA-based molecular markers are stable, intact, abundant in the genome, and free from environmental in uences.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of kale (Brassica oleracea L. var acephala) using agro-morphological and SSR markers

Pipan

Neji

Meglič

et al. 2023

Preprint

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Kale (Brassica oleracea. acephala) is a nutrient-rich green leafy vegetable consumed as food and used in traditional medicine worldwide. An essential step in describing the available genetic resources and ensuring their effective use in breeding programs is to characterize the genetic diversity of available germplasm. In this study, the genetic diversity and structure of 26 kale accessions from South-East Europe were examined using 26 agro-morphological traits collected in the field and 12 SSR markers. Considerable agro-morphological variability was found in most quantitative (CV = 17.26–42.42%) and qualitative (H' = 0.61–1.79) traits. Multifactorial analysis (MFA) showed that country of origin (33.01%) and morphotype (32.30%) significantly influenced kale diversification. Leaf blade shape (20.62%), leaf incision (19.43%), anthocyanin distribution (16.43%), and leaf colour (15.55%) were the traits that most clearly differentiated accessions. The three common commercial kale varieties were identified as independent outliers that differed from the other kale accessions in both MFA and UPGMA clustering analysis. The SSR markers were highly informative with 108 alleles and polymorphic information content ranging from 0.395 to 0.856. Strong genetic diversity was detected at the accession level (H' = 0.58) while genetic differentiation was low (Fst = 0.05). Similar to UPGMA clustering, Bayesian clustering suggests that the kale collection can be divided into four clusters with a high degree of admixture and no geographic grouping pattern is apparent. Overall, the study showed that the kale collection studied represents a valuable reservoir of genetic and agro-morphological variability that could be used for future breeding initiatives.

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Section: Introductionmentioning

confidence: 99%

Genetic diversity of kale (Brassica oleracea L. var acephala) using agro-morphological and SSR markers

Pipan

Neji

Meglič

et al. 2023

Preprint

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“…Plant genomes demonstrate high variability in size and content (Li et al, 2022;Sun et al, 2022). Genome sequences enable studying the beneficial features of agricultural plants and modifying and improving the desired traits (Nützmann et al, 2016;Sedeek et al, 2019;Wang et al, 2020;Choudhury et al, 2022;Singh et al, 2022;Tello-Ruiz et al, 2022). Therefore, plant genomics and pan-genomics open vast opportunities for breeding and agriculture.…”

Section: Introductionmentioning

confidence: 99%

Genome of Linum usitatissimum convar. crepitans expands the view on the section Linum

Dvorianinova,

Pushkova,

Bolsheva

et al. 2023

Front. Genet.

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Sequencing whole plant genomes provides a solid foundation for applied and basic studies. Genome sequences of agricultural plants attract special attention, as they reveal information on the regulation of beneficial plant traits. Flax is a valuable crop cultivated for oil and fiber. Genome sequences of its representatives are rich sources of genetic information for the improvement of cultivated forms of the plant. In our work, we sequenced the first genome of flax with the dehiscence of capsules—Linum usitatissimum convar. сrepitans (Boenn.) Dumort—on the Oxford Nanopore Technologies (ONT) and Illumina platforms. We obtained 23 Gb of raw ONT data and 89 M of 150 + 150 paired-end Illumina reads and tested different tools for genome assembly and polishing. The genome assembly produced according to the Canu—Racon ×2—medaka—POLCA scheme had optimal contiguity and completeness: assembly length—412.6 Mb, N50—5.2 Mb, L50—28, and complete BUSCO—94.6% (64.0% duplicated, eudicots_odb10). The obtained high-quality genome assembly of L. usitatissimum convar. crepitans provides opportunities for further studies of evolution, domestication, and genome regulation in the section Linum.

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“…The main limitation of RAPD markers is their dominant character, which makes it impossible to distinguish homozygotes from heterozygotes. This makes it difficult to estimate the allele frequency, because a more accurate estimate requires the analysis of a large number of individuals, and a low reproducibility of the marker profiles [24,25]. Microsatellite or simple sequence repeat (SSR) markers, most commonly used for plant genotyping, are more informative than other molecular markers because a number of different alleles can exist at a given SSR locus [26].…”

Section: Introductionmentioning

confidence: 99%

Changes in Allele Frequencies and Genetic Diversity in Red Clover after Selection for Cold Tolerance Using SSR Markers

Primorac,

Šarčević,

Knezović

et al. 2023

Agriculture

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The selection of red clover (Trifolium pratense L.) populations adapted to extreme environmental conditions is of great importance due to continuing climate change. The plant material analyzed with simple sequence repeat (SSR) markers included two parent populations, P1 (cultivar ‘Reichersberger’) and P3 (cultivar ‘Croatia’) and their reselections, which were created after one cycle of selection under cold temperature conditions. The reselections PS1 and PS3 were produced by intercrossing 38 surviving plants of parent populations P1 and P3, respectively. A total of 48 plants from each cultivar and each reselection were randomly selected for SSR analysis. Sixteen SSR primer pairs were selected, taking into account the presence of loci on all seven pairs of red clover chromosomes. An increase in the average frequency of alleles from the initial populations to the populations after one cycle of selection was observed, followed by a decrease in the number of alleles. Out of a total of 16 loci, the Waples neutrality test revealed significant frequency changes at 12 loci from P1 to PS1 and 9 loci from P3 to PS3 populations. The genetic diversity in the studied populations did not change significantly after selection, leaving enough genetic variability as a prerequisite for the success of future selection.

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Dissecting the plant genome: through new generation molecular markers

Cited by 16 publications

References 113 publications

Genetic diversity of kale (Brassica oleracea L. var acephala) using agro-morphological and SSR markers

Genetic diversity of kale (Brassica oleracea L. var acephala) using agro-morphological and SSR markers

Genome of Linum usitatissimum convar. crepitans expands the view on the section Linum

Changes in Allele Frequencies and Genetic Diversity in Red Clover after Selection for Cold Tolerance Using SSR Markers

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