Dataset Information

Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping.

ABSTRACT: The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co-segregating marker.

SUBMITTER: Vigna BB

PROVIDER: S-EPMC4841517 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping.

Vigna Bianca B Z BB Santos Jean C S JC Jungmann Leticia L do Valle Cacilda B CB Mollinari Marcelo M Pastina Maria M MM Pagliarini Maria Suely MS Garcia Antonio A F AA Souza Anete P AP

PloS one 20160422 4

The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a f ...[more]

PMID: 27104622

Similar Datasets

Project description:Urochloa humidicola is a warm-season grass commonly used as forage in the tropics and is recognized for its tolerance to seasonal flooding. This grass is an important forage species for the Cerrado and Amazon regions of Brazil. U. humidicola is a polyploid species with variable ploidy (6X-9X) and facultative apomixis with high phenotypic plasticity. However, this apomixis and ploidy, as well as the limited knowledge of the genetic basis of the germplasm collection, have constrained genetic breeding activities, yet microsatellite markers may enable a better understanding of the species' genetic composition. This study aimed to develop and characterize new polymorphic microsatellite molecular markers in U. humidicola and to evaluate their transferability to other Urochloa species.A set of microsatellite markers for U. humidicola was identified from two new enriched genomic DNA libraries: the first library was constructed from a single sexual genotype and the second from a pool of eight apomictic genotypes selected on the basis of previous results. Of the 114 loci developed, 72 primer pairs presented a good amplification product, and 64 were polymorphic among the 34 genotypes tested. The number of bands per simple sequence repeat (SSR) locus ranged from 1 to 29, with a mean of 9.6 bands per locus. The mean polymorphism information content (PIC) of all loci was 0.77, and the mean discrimination power (DP) was 0.87. STRUCTURE analysis revealed differences among U. humidicola accessions, hybrids, and other Urochloa accessions. The transferability of these microsatellites was evaluated in four species of the genus, U. brizantha, U. decumbens, U. ruziziensis, and U. dictyoneura, and the percentage of transferability ranged from 58.33% to 69.44% depending on the species.This work reports new polymorphic microsatellite markers for U. humidicola that can be used for breeding programs of this and other Urochloa species, including genetic linkage mapping, quantitative trait loci identification, and marker-assisted selection.

Project description:BACKGROUND AND AIMS:The perennial C4 grass Urochloa humidicola is widely planted on infertile acidic and waterlogging-prone soils of tropical America. Waterlogging results in soil anoxia, and O2 deficiency can reduce nutrient uptake by roots. Interestingly, both nutrient deficiencies and soil waterlogging can enhance root cortical cell senescence, and the increased gas-filled porosity facilitates internal aeration of roots. We tested the influence of nutrient supply and root-zone O2 on root traits, leaf nutrient concentrations and growth of U. humidicola. METHODS:Plants were grown in pots in a completely randomized design under aerated or stagnant deoxygenated hydroponic conditions and six nutrient regimes, with low to high concentrations of all essential elements, for 28 d in a controlled-temperature greenhouse. The standard acid solution (SAS) used was previously designed based on infertile acidic soils of the tropical America savannas, and step increases in the concentration of SAS were used in aerated or deoxygenated 0.1 % agar solution, which mimics changes in gas composition in waterlogged soils. Measurements included shoot and root growth, root porosity, root anatomy, radial O2 loss, and leaf tissue nutrient concentrations. KEY RESULTS:Shoot dry mass was reduced for plants in stagnant compared with aerated conditions at high, but not at low, levels of mineral nutrition. In low-nutrition stagnant solution, roots were shorter, of greater porosity and had smaller radial thickness of the stele. Suberized lamellae and lignified sclerenchyma, as well as a strong barrier to radial O2 loss, were documented for roots from all treatments. Leaf nutrient concentrations of K, Mg and Ca (but not N, P and S) were higher in aerated than in stagnant conditions. CONCLUSIONS:Under low-nutrient conditions, plant growth in stagnant solution was equal to that in aerated solution, whereas under higher-nutrient regimes growth increased but dry mass in stagnant solution was less than in aerated solution. Slow growth in low-nutrient conditions limited any further response to the low O2 treatment, and greater porosity and smaller stele size in roots would enhance internal O2 movement within roots in the nutrient-limited stagnant conditions. A constitutive barrier to radial O2 loss and aerenchyma facilitates O2 movement to the tips of roots, which presumably contributes to maintaining nutrient uptake and the tolerance of U. humidicola to low O2 in the root-zone.

Project description:BACKGROUND: Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. RESULTS: Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM. Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. CONCLUSION: Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and refine assembly of bovine genome sequence. Even after the bovine genome is completely sequenced, the map will continue to be a useful tool to link observable phenotypes and animal genotypes to underlying genes and molecular mechanisms influencing economically important beef and dairy traits.

Dataset Information

Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping.

Publications

Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets