An Operational SNP Panel Integrated to SSR Marker for the Assessment of Genetic Diversity and Population Structure of the Common Bean

Müller, Bárbara S. F.; Παππάς, Γεώργιος; Valdisser, P. A. M. R.; Coelho, G. R. C.; Menezes, Ivandilson Pessoa Pinto de; Abreu, A. G. de; Borba, T. C. de O.; Sakamoto, Tetsu; Brondani, C.; Barros, Everaldo Gonçalves de; Vianello, R. P.

doi:10.1007/s11105-015-0866-x

Cited by 25 publications

(25 citation statements)

References 69 publications

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“…Genotyping for the 384 SNPs was done using the Vera Code ® BeadXpress platform (Illumina) at the Biotechnology Laboratory of Embrapa Arroz e Feijão (Goiania, GO, Brazil). A set of 384 SNP markers, validated through Prelim file ( https://icom.illumina.com/Custom/UploadOpaPrelim/ ) previously identified for P. vulgaris ( Müller et al , 2015 ) and derivatives of polymorphism between the lines BAT 477 of Mesoamerican origin and Jalo EEP558 of Andean origin were selected to compose the Oligo Pool Assay (OPA) SNP markers.…”

Section: Methodsmentioning

confidence: 99%

Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers

et al. 2017

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The common bean is characterized by high sensitivity to drought and low productivity. Breeding for drought resistance in this species involves genes of different genetic groups. In this work, we used a SEA 5 x AND 277 cross to map quantitative trait loci associated with drought tolerance in order to assess the factors that determine the magnitude of drought response in common beans. A total of 438 polymorphic markers were used to genotype the F8 mapping population. Phenotyping was done in two greenhouses, one used to simulate drought and the other to simulate irrigated conditions. Fourteen traits associated with drought tolerance were measured to identify the quantitative trait loci (QTLs). The map was constructed with 331 markers that covered all 11 chromosomes and had a total length of 1515 cM. Twenty-two QTLs were discovered for chlorophyll, leaf and stem fresh biomass, leaf biomass dry weight, leaf temperature, number of pods per plant, number of seeds per plant, seed weight, days to flowering, dry pod weight and total yield under well-watered and drought (stress) conditions. All the QTLs detected under drought conditions showed positive effects of the SEA 5 allele. This study provides a better understanding of the genetic inheritance of drought tolerance in common bean.

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Section: Methodsmentioning

confidence: 99%

Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers

et al. 2017

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“…Diverse researchers around the world use local populations or samples of common bean landraces as reference sets to study their genetic diversity and population structure [6,7,32,33,34]. Nevertheless, such on-farm crop genetic diversity is highly dynamic as a result of the agroecological conditions of cultivation, the preferences of farmers in seed selection and the management of seed lots, among other factors, that have important impacts on the population structure and chemical composition of the grain, which change across time [5,24,33,35].…”

Section: Diversity Of Common Bean Landraces Using Agro-morphological mentioning

confidence: 99%

Diversity of Common Bean (Phaseolus vulgaris L.) Landraces and the Nutritional Value of their Grains

Chávez-Servia¹,

Heredia-García²,

NetzahualcoyotlMayek-Pérez³

et al. 2016

Grain Legumes

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Grain legumes are considered major sources of dietary proteins, calories, certain minerals and vitamins, and they are the most widely cultivated and consumed crops worldwide. Among them are the common beans, whose major production volumes came from landraces cultivated in traditional farming systems. The objective of this study was to evaluate the phenotypic diversity of a set of common bean landraces from Mexico based on the agromorphological traits and nutritional composition of the grain in the context of traditional farming systems. Different field and laboratory data were collected and complemented with secondary information published in refereed journals and research reports. The results showed that there are significant differences in the morphological and physiological traits of the plant, pod and grain among groups of common bean landraces of different geographic origins, which were associated with different indigenous groups. Similar patterns were observed in the contents of anthocyanins, polyphenols, flavoinds and minerals as well as antioxidant activity. In the evaluated population groups in each region, there are outstanding populations in terms of agromorphological traits and the nutritional value of the grain that can enable a participatory breeding initiative guided by regional objectives. Some populations from Sierra Norte, Oaxaca, presented higher values in Zn and Fe, and populations from Estado de Mexico exhibited high polyphenol and flavonoid values but stable agronomic behaviour.

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“…These two types of marker bring different views of the structure, and the merits of each are listed in Guichoux et al (2011). SSRs and SNPs were compared in order to assess population structure and relatedness in short-lived species such as rice (Singh et al 2013), maize (Hamblin et al 2007;Van Inghelandt et al 2010;Yang et al 2011), sunflower (Filippi et al 2015), bean (Müller et al 2015), and cowpea (Desalegne et al 2017). These comparisons are rarer for perennials (grapes (Emanuelli et al 2013) and jujube (Chen et al 2017)).…”

Section: Introductionmentioning

confidence: 99%

Comparison of structure analyses and core collections for the management of walnut genetic resources

Bernard

Barreneche

Donkpegan

et al. 2020

Tree Genetics & Genomes

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The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods based on different algorithms (“maximum length subtree” and “entry-to-nearest-entry” methods). We showed that core collections based on few SSR markers are able to capture at least 99.5% of the SNP allelic diversity, irrespective of the construction method used. Then, core collections based on each marker type are highly similar, using both construction methods. All these steps are crucial to identify the suitable tools and methods to improve plant genetic resources management.

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An Operational SNP Panel Integrated to SSR Marker for the Assessment of Genetic Diversity and Population Structure of the Common Bean

Cited by 25 publications

References 69 publications

Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers

Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers

Diversity of Common Bean (Phaseolus vulgaris L.) Landraces and the Nutritional Value of their Grains

Comparison of structure analyses and core collections for the management of walnut genetic resources

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