The five Urochola spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

Background and Aims: Urochola (syn. Brachiaria, and including some Panicum and Megathyrus) is a genus of tropical and subtropical grasses widely sown as forage to feed ruminants in the tropics. A better understanding of the diversity among Urochola spp. allow us to leverage its varying ploidy levels and genome composition to accelerate its improvement, following the example from other crop genera. Methods: We explored the genetic make-up and population structure in 111 accessions, which comprise the five Urochola species used for the development of commercial cultivars. These accessions are conserved from wild materials from collection sites at their centre of origin in Africa. We used RNA-seq, averaging 40M reads per accession, to generate 1,167,542 stringently selected SNP markers that tentatively encompassed the complete Urochola gene pool used in breeding. Key Results: We identified ten subpopulations, which had no relation with geographical origin and represented ten independent gene pools, and two groups of admixed accessions. Our results support a division in U. decumbens by ploidy, with a diploid subpopulation closely related to U. ruziziensis, and a tetraploid subpopulation closely related to U. brizantha. We observed highly differentiated gene pools in U. brizantha, which were not related with origin or ploidy. Particularly, one U. brizantha subpopulation clustered distant from the other U. brizantha and U. decumbens subpopulations, so likely containing unexplored alleles. We also identified a well-supported subpopulation containing both polyploid U. decumbens and U. brizantha accessions; this was the only group containing more than one species and tentatively constitutes an independent "mixed" gene pool for both species. We observed two gene pools in U. humidicola. One subpopulation, "humidicola-2", was much less common but likely includes the only known sexual accession in the species. Conclusions: Our results offered a definitive picture of the available diversity in Urochola to inform breeding and resolve questions raised by previous studies. It also allowed us identifying prospective founders to enrich the breeding gene pool and to develop genotyping and genotype-phenotype association mapping experiments.

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Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

BMC Plant Biology ◽

10.1186/s12870-021-02932-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zhengjie Chen ◽

Dengguo Tang ◽

Jixing Ni ◽

Peng Li ◽

Le Wang ◽

...

Keyword(s):

Marker Assisted Selection ◽

Inbred Lines ◽

Average Density ◽

Snp Markers ◽

Data Sets ◽

Rna Seq ◽

Specific Pcr ◽

Maize Inbred Lines ◽

Allele Specific ◽

Allele Specific Pcr

Abstract Background Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

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Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l.

Genes ◽

10.3390/genes12070957 ◽

2021 ◽

Vol 12 (7) ◽

pp. 957

Author(s):

Paulina Tomaszewska ◽

Till K. Pellny ◽

Luis M. Hernández ◽

Rowan A. C. Mitchell ◽

Valheria Castiblanco ◽

...

Keyword(s):

Flow Cytometry ◽

Germplasm Collection ◽

Forage Grass ◽

Breeding Programs ◽

Robust Identification ◽

Ploidy Levels ◽

Sustainable Improvement ◽

Tropical Forage ◽

Relative Differences

Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. We aimed to develop an optimized approach to determine ploidy of germplasm collection of this tropical forage grass group using dried leaf material, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Our methods enable robust identification of ploidy levels (coefficient of variation of G0/G1 peaks, CV, typically <5%). Ploidy of some 348 forage grass accessions (ploidy range from 2x to 9x), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes are used in the current breeding programs at CIAT and EMBRAPA: the ’brizantha’ and ’humidicola’ agamic complexes are variable, with multiple ploidy levels. Some U. brizantha accessions have odd level of ploidy (5x), and the relative differences in fluorescence values of the peak positions between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed aneuploidy.

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Machine learning, transcriptome, and genotyping chip analyses provide insights into SNP markers identifying flower color in Platycodon grandiflorus

Scientific Reports ◽

10.1038/s41598-021-87281-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Go-Eun Yu ◽

Younhee Shin ◽

Sathiyamoorthy Subramaniyam ◽

Sang-Ho Kang ◽

Si-Myung Lee ◽

...

Keyword(s):

Machine Learning ◽

Random Forest ◽

Feature Selection Method ◽

Flower Color ◽

Classification Performance ◽

Snp Markers ◽

Rna Seq ◽

Color Classification ◽

Dna Pcr ◽

Selection Of

AbstractBellflower is an edible ornamental gardening plant in Asia. For predicting the flower color in bellflower plants, a transcriptome-wide approach based on machine learning, transcriptome, and genotyping chip analyses was used to identify SNP markers. Six machine learning methods were deployed to explore the classification potential of the selected SNPs as features in two datasets, namely training (60 RNA-Seq samples) and validation (480 Fluidigm chip samples). SNP selection was performed in sequential order. Firstly, 96 SNPs were selected from the transcriptome-wide SNPs using the principal compound analysis (PCA). Then, 9 among 96 SNPs were later identified using the Random forest based feature selection method from the Fluidigm chip dataset. Among six machines, the random forest (RF) model produced higher classification performance than the other models. The 9 SNP marker candidates selected for classifying the flower color classification were verified using the genomic DNA PCR with Sanger sequencing. Our results suggest that this methodology could be used for future selection of breeding traits even though the plant accessions are highly heterogeneous.

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Genetic diversity of common bean (Phaseolus vulgaris L.) breeding collection in Serbia

Genetika ◽

10.2298/gensr1901001s ◽

2019 ◽

Vol 51 (1) ◽

pp. 1-15 ◽

Cited By ~ 2

Author(s):

Aleksandra Savic ◽

Milka Brdar-Jokanovic ◽

Miodrag Dimitrijevic ◽

Sofija Petrovic ◽

Milan Zdravkovic ◽

...

Keyword(s):

Common Bean ◽

Gene Pool ◽

Gene Diversity ◽

Principal Component ◽

Molecular Data ◽

Phenotypic Traits ◽

Gene Pools ◽

Vegetable Crops ◽

Novi Sad

The characterization of 41 common bean cultivars and landraces from breeding collection of Institute of Field and Vegetable Crops, Novi Sad, Serbia, was done based on phenotypic traits and microsatellite markers. Phenotypic traits were chosen from Bioversity International descriptor list. In addition, main yield components were investigated. Analysis of phaseolin type revealed affiliation of cultivars and landraces to Mesoamerican or Andean gene pool. Cultivars and landraces demonstrated significant diversity level with regard to studied phenotypic traits. Identified variation showed high potential for developing new cultivars with desirable combination of traits. Principal component analysis based on phenotypic traits separated bean cultivars and landraces in two groups, which corresponded to Mesoamerican and Andean determined according to phaseolin type. Putative hybrids, with combination of traits between gene pools were also identified. Analysis of microsatellite data, using twenty-two SSR primer pairs, showed medium gene diversity in studied material. Microsatellite-based cluster analysis separated genotypes in two discrete clusters and several subclusters. No clear separation according to gene pool was found between the clusters, however grouping according to gene pool and patterns of phenotypic variation, following these gene pools, were observed within subclusters. Knowledge on detailed relationships of cultivars and landraces based on phenotypic and molecular data would facilitate identification of candidates for future breeding.

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Molecular Hallmarks, Agronomic Performances and Seed Nutraceutical Properties to Exploit Neglected Genetic Resources of Common Beans Grown by Organic Farming in Two Contrasting Environments

Frontiers in Plant Science ◽

10.3389/fpls.2021.674985 ◽

2021 ◽

Vol 12 ◽

Author(s):

Pietro Sica ◽

Francesco Scariolo ◽

Aline Galvao ◽

Domiziana Battaggia ◽

Carlo Nicoletto ◽

...

Keyword(s):

Genetic Resources ◽

Common Bean ◽

Sea Level ◽

Seed Yield ◽

Molecular Genetic ◽

Snp Markers ◽

Gene Pools ◽

Crop Species ◽

Pure Lines ◽

Nutraceutical Properties

Common bean (Phaseolus vulgaris L.) is an essential source of food proteins and an important component of sustainable agriculture systems around the world. Thus, conserving and exploiting the genetic materials of this crop species play an important role in achieving global food safety and security through the preservation of functional and serependic opportunities afforded by plant species diversity. Our research aimed to collect and perform agronomic, morpho-phenological, molecular-genetic, and nutraceutical characterizations of common bean accessions, including lowland and mountain Venetian niche landraces (ancient farmer populations) and Italian elite lineages (old breeder selections). Molecular characterization with SSR and SNP markers grouped these accessions into two well-separated clusters that were linked to the original Andean and Mesoamerican gene pools, which was consistent with the outputs of ancestral analysis. Genetic diversity in the two main clusters was not distributed equally the Andean gene pool was found to be much more uniform than the Mesoamerican pool. Additional subdivision resulted in subclusters, supporting the existence of six varietal groups. Accessions were selected according to preliminary investigations and historical records and cultivated in two contrasting Venetian environments: sea-level and mountain territories. We found that the environment significantly affected some nutraceutical properties of the seeds, mainly protein and starch contents. The antioxidant capacity was found significantly greater at sea level for climbing accessions and in the mountains for dwarf accessions. The seed yield at sea level was halved than mountain due to a seeds reduction in weight, volume, size and density. At sea level, bean landraces tended to have extended flowering periods and shorter fresh pod periods. The seed yield was positively correlated with the length of the period during which plants had fresh pods and negatively correlated with the length of the flowering period. Thus, the agronomic performance of these genetic resources showed their strong connection and adaptation to mountainous environments. On the whole, the genetic-molecular information put together for these univocal bean entries was combined with overall results from plant and seed analyses to select and transform the best accessions into commercial varieties (i.e., pure lines) suitable for wider cultivation.

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Tropical forage trees with low potential defaunating capacity

Proceedings of the British Society of Animal Science ◽

10.1017/s1752756200011327 ◽

2005 ◽

Vol 2005 ◽

pp. 221-221

Author(s):

G. E. Monforte Briceño ◽

C. A. Sandoval Castro ◽

C. M. Capetillo Leal ◽

L. Ramírez Avilés

Keyword(s):

Batch Culture ◽

Culture System ◽

Potential Effect ◽

Rumen Protozoa ◽

Tropical Forage ◽

Livestock Feeding ◽

The Tropics ◽

Tropical Systems

Forage trees are commonly use for livestock feeding in the tropics. It is known that some species can affect the rumen protozoa population (Odenyoet al., 1997). However, little is known about the potential effect upon rumen protozoa of several species which are also use as feed in tropical systems. The objective of the experiment was to assess the defaunating capacity of forage trees. In companion reports (Monforteet al., 2005) we reported plants with a potential defaunating effect as evaluated under an in vitro batch culture system (Sandovalet al., 2005). Here we present those plants which did not have or had low effect on protozoa population in anin vitroculture.

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The genetic make-up of the European landraces of the common bean

Plant Genetic Resources ◽

10.1017/s1479262111000190 ◽

2011 ◽

Vol 9 (2) ◽

pp. 197-201 ◽

Cited By ~ 14

Author(s):

S. A. Angioi ◽

D. Rau ◽

L. Nanni ◽

E. Bellucci ◽

R. Papa ◽

...

Keyword(s):

Common Bean ◽

Gene Pool ◽

Chloroplast Microsatellites ◽

Gene Pools ◽

Mesoamerican Gene Pool ◽

Hybridization Event ◽

South Eastern Europe ◽

Andean Type ◽

The Common ◽

African Sample

Here, we present a brief overview of the main studies conducted on the common bean (Phaseolus vulgaris L.) in Europe and other countries outside its centres of origin. We focus on the proportions of the Andean and Mesoamerican gene pools, and on the inter-gene pool hybridization events. In Europe, for chloroplast microsatellites, 67% of European germplasm is of Andean origin. Within Europe, interesting trends have been seen; indeed, the majority of the Andean type is found in the three macro-areas of the Iberian Peninsula, Italy and central-northern Europe, while, in eastern and south-eastern Europe, the proportion of the Mesoamerican type increased. On a local scale, the contribution of the Mesoamerican type is always low. On other continents, various situations are seen using different markers: in China and Brazil, the Mesoamerican gene pool prevails, while in an African sample, overall, both gene pools are equally represented, with differences in individual countries. The frequency of European bean genotypes deriving from at least one hybridization event was 44% with an uneven distribution. Interestingly, hybrids tend to have intermediate seed size in comparison with ‘pure’ Andean or Mesoamerican types. On other continents, very few hybrids are found, probably because of the different marker systems used.

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RNA-Seq-Mediated Transcriptome Analysis of a Fiberless Mutant Cotton and Its Possible Origin Based on SNP Markers

PLoS ONE ◽

10.1371/journal.pone.0151994 ◽

2016 ◽

Vol 11 (3) ◽

pp. e0151994 ◽

Cited By ~ 13

Author(s):

Qifeng Ma ◽

Man Wu ◽

Wenfeng Pei ◽

Xiaoyan Wang ◽

Honghong Zhai ◽

...

Keyword(s):

Transcriptome Analysis ◽

Snp Markers ◽

Rna Seq

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Genetic diversity of Colombian landraces of common bean as detected through the use of silver-stained and fluorescently labelled microsatellites

Plant Genetic Resources ◽

10.1017/s1479262110000420 ◽

2011 ◽

Vol 9 (01) ◽

pp. 86-96 ◽

Cited By ~ 17

Author(s):

Lucy M. Díaz ◽

Héctor F. Buendía ◽

Myriam C. Duque ◽

Matthew W. Blair

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Common Bean ◽

Gene Pool ◽

Major Gene ◽

Gene Pools ◽

Silver Stain ◽

Fluorescent Marker ◽

Fluorescent Markers

Colombia, situated at the northern end of the Andes mountains of South America and in proximity to Central America, is an important centre of diversity for common bean (Phaseolus vulgarisL.) that has a mix of cultivated germplasm from both major gene pools (Andean and Mesoamerican) for the species. Microsatellites are a useful marker system for analyzing genetic diversity of this crop and can be analyzed with manual (silver-stain) or automated (ABI) detection systems and using unlabelled or fluorescently labelled markers, respectively. The objectives of this research were to evaluate the genetic diversity of 92 Colombian landraces and gene pool controls with 36 fluorescent and 30 non-fluorescent microsatellite markers and to determine the extent of introgression between the Andean and Mesoamerican gene pools for this germplasm. A comparison of fluorescentversusnon-fluorescent marker systems was performed with 14 loci, which were evaluated with both methods; the fluorescent markers were found to be more precise than the non-fluorescent markers in determining population structure. A combined analysis of 52 microsatellites using the 36 fluorescent markers and 16 non-overlapping, silver-stained markers produced an accurate population structure for the Andean gene pool that separated race Nueva Granada and race Peru genotypes and clearly identified introgression between these races and the gene pools. The results of this research are important for the application of microsatellite markers to diversity analysis in common bean and for the conservation of landraces in Colombia and neighbouring countries of Latin America, where similar germplasm exists and where gene pool or race mixtures also occur.

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