Classification and Characterization of Species within the Genus Lens Using Genotyping-by-Sequencing (GBS)

Wong, Melissa M L; Gujaria-Verma, Neha; Ramsay, Larissa; Yuan, Huajun; Caron, Carolyn T.; Diapari, Marwan; Vandenberg, Albert; Bett, Kirstin E.

doi:10.1371/journal.pone.0122025

Cited by 113 publications

(150 citation statements)

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“…The major difference between the population structure and phylogenetic analyses was the former used the whole exome capture data, which constitutes about 6,680,000 variants, whereas less than 1% of the total variants were used in the latter. In either case, the results match well with what is known of the relationships from the previous studies (Mayer and Soltis, 1994; Sonnante et al., 2003; Wong et al., 2015). …”

Section: Discussionmentioning

confidence: 99%

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Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

et al. 2018

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Premise of the StudyLentil is an important legume crop with reduced genetic diversity caused by domestication bottlenecks. Due to its large and complex genome, tools for reduced representation sequencing are needed. We developed an exome capture array for use in various genetic diversity studies.MethodsBased on the CDC Redberry draft genome, we developed an exome capture array using multiple sources of transcript resources. The probes were designed to target not only the cultivated lentil, but also wild species. We assessed the utility of the developed method by applying the generated data set to population structure and phylogenetic analyses.ResultsThe data set includes 16 wild lentils and 22 cultivar accessions of lentil. Alignment rates were over 90%, and the genic regions were well represented in the capture array. After stringent filtering, 6.5 million high‐quality variants were called, and the data set was used to assess the interspecific relationships within the genus Lens.DiscussionThe developed exome capture array provides large amounts of genomic data to be used in many downstream analyses. The method will have useful applications in marker‐assisted breeding programs aiming to improve the quality of cultivated lentil.

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Section: Discussionmentioning

confidence: 99%

“…(Fabaceae subfam. Papilionoideae, tribe Vicieae) consists of seven species, divided into four gene pools with respect to their ability to make crosses with the cultivated lentil (Wong et al., 2015). The crosses within the primary gene pool ( L. culinaris , L. orientalis Popow, and L. tomentosus Ladiz.)…”

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Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

et al. 2018

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“…To address the challenge of resolving the phylogenetic relationships among very closely related species, large genome-scale data sets can be used [45]. Reduced-representation methods provide powerful and cost-effective tools, producing abundant large-scale genomic data [46] and have been used in many phylogenetic studies [45, 47–51]. …”

Section: Introductionmentioning

confidence: 99%

“…A large number of variants are generated by GBS [53] and have been applied to a wide range of crops such as barley [54], lentils [51], maize [55], potato [56], reed canarygrass [57], rice [58], soybean [59], switchgrass [60], and wheat [61]. GBS has been used to infer the classification of wild species like chickpea [62], lentils [51], sedges [45], and tomatoes [63]. …”

Section: Introductionmentioning

confidence: 99%

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

et al. 2016

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BackgroundThe majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex.ResultsWe used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30% missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) rate of missing data 30%, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic.ConclusionsOur study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0806-x) contains supplementary material, which is available to authorized users.

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“…Utilization of different genotypes with very high and very low mineral concentrations may be used to develop mapping populations used to identify QTL associated with these micronutrients in lentil. Genomic approaches (Kaur et al, 2011;Verma et al, 2013;Sharpe et al, 2013;Wong et al, 2015) could be used to map or tag genes involved in seed mineral concentration in lentil and for precise introgression of novel traits from the Lens species and wild relatives.…”

Section: Resultsmentioning

confidence: 99%

Genetic diversity among cultivated and wild lentils for iron, zinc, copper, calcium and magnesium concentrations

Gupta¹,

Thavarajah²,

McGee³

et al. 2016

Aust J Crop Sci

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Information on the seed mineral concentration of cultivated and wild lentils is limited. The objective of this study was to determine the concentrations of iron (Fe), zinc (Zn), calcium (Ca), copper (Cu), and magnesium (Mg) in the seeds of 26 lentil genotypes representing 4 species and 3 subspecies of Lens. Plants were grown in a greenhouse using a completely randomized design with three replicates (n=78). Seed mineral concentrations were measured using acid digestion followed by inductively coupled plasma-optical emission spectroscopy. Concentrations of Fe, Zn, Ca, Cu, and Mg in seeds varied from 26-92, 17-51, 97-536, 3-12 and 272-892 mg kg -1 , respectively, among the Lens culinaris genotypes. Mineral concentrations for L. lamottei (Fe=64-80, Zn=26-40, Ca=311-434, Cu=2-6, Mg=754-839 mg kg -1 ), L. nigricans (60-70, 33-39, 508-590, 3-4, 445-738 mg kg -1 ) and L. ervoides (65, 37, 339, 6, 638 mg kg -1 ) were within the range of Lens culinaris genotypes. No wild species was superior to cultivated ones for all micronutrients. A larger set of germplasm should be evaluated in future experiments to identify additional genetic variation in lentil for these micronutrients.

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Classification and Characterization of Species within the Genus Lens Using Genotyping-by-Sequencing (GBS)

Cited by 113 publications

References 69 publications

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

Genetic diversity among cultivated and wild lentils for iron, zinc, copper, calcium and magnesium concentrations

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