Genetic variation of the granule-bound starch synthase I (GBSSI) genes in waxy and non-waxy accessions of Chenopodium berlandieri ssp. nuttalliae from Central Mexico

2015 ◽  
Vol 14 (1) ◽  
pp. 57-66
Author(s):  
Verónica Cepeda-Cornejo ◽  
Douglass C. Brown ◽  
Guadalupe Palomino ◽  
Eulogio de la Cruz ◽  
Melissa Fogarty ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Chenopodium Quinoa ◽  
Seed Morphology ◽  
Starch Synthase ◽  
Null Alleles ◽  
Central Mexico ◽  
B Genome ◽  
A Genome ◽  
Chenopodium Berlandieri ◽  
Granule Bound Starch Synthase

Huauzontle (Chenopodium berlandieri ssp. nuttalliae) is a locally important vegetable crop native to the highland valleys of Central Mexico and a potential source of genes for improving its Andean sister crop, quinoa (Chenopodium quinoa). A previous work involving two huauzontle lines identified one waxy genotype that lacked amylose due to mutations in granule-bound starch synthase I (GBSSI), major amylose-synthesis genes with two constituent subgenomes, A and B. We conducted this study to determine the extent of waxy genotypes and cryptic GBSSI mutations in 11 huauzontle accessions or landrace populations extending from Puebla in the southeast to Jalisco in the northwest. This represents one of the first published studies of genetic variation in C. berlandieri ssp. nuttalliae. Accessions were phenotyped for opaque versus translucent seed morphology and their seed starches were stained with Lugol's Stain. In addition, complete or partial GBSSI genes from their A and B genomes were polymerase chain reaction (PCR)-amplified, cloned and sequenced. Seven accessions were either wholly or partially non-waxy while six were either entirely or partially waxy. All waxy accessions carried the same putatively null alleles, designated gbssIa-tp (A-genome) and gbssIb-del (B-genome). The identification of publicly available genotypes carrying gbssIa-tp and their potential use in breeding waxy grain quinoa is discussed.

scholarly journals Phylogenetic analysis of 23 accessions of Indonesian banana cultivars based on Internal Transcribed Spacer 2 (ITS2) region

2020 ◽  
Vol 25 (1) ◽  
pp. 1
Author(s):  
Karlia Meitha ◽  
Intan Fatmawati ◽  
Fenny Martha Dwivany ◽  
Agus Sutanto ◽  
Sigit Nur Pratama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Internal Transcribed Spacer ◽  
Molecular Breeding ◽  
Future Research ◽  
Its2 Region ◽  
Phylogenetic Tree Analysis ◽  
Multiple Sequence ◽  
B Genome ◽  
A Genome

Pisang Kepok (Musa spp. [ABB ’Saba’ subgroup]) has several unique characteristics, such as tolerance to drought and Fusarium Foc (TR4) disease. Currently, the genetic diversity of Pisang Kepok in Indonesia is not well identified, although it is widely cultivated. Information on genetic diversity is essential for developing breeding strategies to achieve efficient cultivar improvement in the future. Aims of this research were to analyze the genetic variation of Pisang Kepok from some islands in Indonesia and to determine the genetic relationship between Pisang Kepok and other accessions banana cultivars based on ITS2 region, as a basis for future research in improving banana quality through molecular breeding. We have conducted the multiple sequence alignment and built the phylogenetic tree analysis using the Bayesian Inference Phylogeny method of one million generations (ngen = 1,000,000). The ITS2 region showed two clade ingroups: first clade consists of banana with B genome (balbisiana), while the second clade consists of banana with only A genome (acuminata). In general, all accessions of Pisang Kepok cultivars were clustered in the B genome of bananas cultivars. In addition, the ITS2 sequences and secondary structures among Pisang Kepok from various regions are identical, suggesting that there was no genetic variation in the ITS2 region of Pisang Kepok from multiple areas in Indonesia.

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

scholarly journals A Microsatellite Map of Wheat

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2007-2023 ◽  
Author(s):  
Marion S Röder ◽  
Victor Korzun ◽  
Katja Wendehake ◽  
Jens Plaschke ◽  
Marie-Hélène Tixier ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Reference Population ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
D Genome ◽  
B Genome ◽  
Microsatellite Map ◽  
A Genome ◽  
Polymorphic Microsatellite ◽  
Primer Sets

Abstract Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

scholarly journals Three founding ancestral genomes involved in the origin of sugarcane

2021 ◽  
Author(s):  
Nicolas Pompidor ◽  
Carine Charron ◽  
Catherine Hervouet ◽  
Stéphanie Bocs ◽  
Gaëtan Droc ◽  
...  
Keyword(s):  
Evolutionary Model ◽  
Saccharum Officinarum ◽  
Modern Cultivar ◽  
Ploidy Levels ◽  
Saccharum Spp ◽  
Bac Clones ◽  
B Genome ◽  
A Genome ◽  
Genomic Regions ◽  
Complex Genome

Abstract Background and Aims Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. Key Results The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. Conclusions This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior inDrosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 283-294 ◽  
Author(s):  
Kristie Ashton ◽  
Ana Patricia Wagoner ◽  
Roland Carrillo ◽  
Greg Gibson
Keyword(s):  
Heart Rate ◽  
Genetic Variation ◽  
Recombinant Inbred Lines ◽  
Model Organism ◽  
Interval Mapping ◽  
Activity Levels ◽  
Environmental Variance ◽  
Genome Wide ◽  
A Genome ◽  
Monoamine Receptors

AbstractDrosophila melanogaster appears to be well suited as a model organism for quantitative pharmacogenetic analysis. A genome-wide deficiency screen for haploinsufficient effects on prepupal heart rate identified nine regions of the genome that significantly reduce (five deficiencies) or increase (four deficiencies) heart rate across a range of genetic backgrounds. Candidate genes include several neurotransmitter receptor loci, particularly monoamine receptors, consistent with results of prior pharmacological manipulations of heart rate, as well as genes associated with paralytic phenotypes. Significant genetic variation is also shown to exist for a suite of four autonomic behaviors that are exhibited spontaneously upon decapitation, namely, grooming, grasping, righting, and quivering. Overall activity levels are increased by application of particular concentrations of the drugs octopamine and nicotine, but due to high environmental variance both within and among replicate vials, the significance of genetic variation among wild-type lines for response to the drugs is difficult to establish. An interval mapping design was also used to map two or three QTL for each behavioral trait in a set of recombinant inbred lines derived from the laboratory stocks Oregon-R and 2b.

Putative diploid ancestors of 80-chromosome Glycine tabacina

Genome ◽  
1992 ◽  
Vol 35 (1) ◽  
pp. 140-146 ◽  
Author(s):  
R. J. Singh ◽  
K. P. Kollipara ◽  
F. Ahmad ◽  
T. Hymowitz
Keyword(s):  
Adventitious Roots ◽  
Chromosome Doubling ◽  
Colchicine Treatment ◽  
Meiotic Pairing ◽  
B Genome ◽  
Specific Hybridization ◽  
A Genome ◽  
Genome Homology ◽  
Glycine Tabacina ◽  
Natural Mutation

The objective of this study was to discover the diploid progenitors of 80-chromosome Glycine tabacina with adventitious roots (WAR) and no adventitious roots (NAR). Three synthetic amphiploids were obtained by somatic chromosome doubling. These were (i) (G. latifolia, 2n = 40, genome B1B1,) × (G. microphylla, 2n = 40, genome BB) = F1(2n = 40, genome BB1) – 0.1% colchicine treatment (CT) – 2n = 80, genome BBB1B1; (ii) (G. canescens, 2n = 40, genome AA) × G. microphylla, 2n = 40, genome BB) = F1 (2n = 40, genome AB) – (CT) – 2n = 80, genome AABB; (iii) (G. latifolia, 2n = 40, B1B1) × G. canescens, 2n = 40, AA) = F1 (2n = 40, genome AB1) – (CT) – 2n = 80, genome AAB1B1. The segmental allotetraploid BBB1B1 was morphologically similar to the 80-chromosome G. tabacina (WAR), but meiotic pairing data in F1 hybrids did not support the complete genomic affinity. Despite normal diploid-like meiosis in allotetraploids AABB and AAB1B1, AABB was completely fertile, while pod set in AAB1B1 was very sparse. Morphologically, allotetraploid AABB was indistinguishable from the 80-chromosome G. tabacina (NAR) but in their F1 hybrids, the range of univalents at metaphase I was wide (4–44). The allotetraploid AAB1B1 did not morphologically resemble the 80-chromosome G. tabacina (NAR). However, the F1 hybrid of AABB × AAB1B1 showed normal meiosis with an average chromosome association (range) of 1.7 I (0–4) + 39.2 II (38–40). Based on this information, we cannot correctly deduce the diploid progenitor species of the 80-chromosome G. tabacina (NAR). The lack of exact genome homology may be attributed to the geographical isolation, natural mutation, and growing environmental conditions since the inception of 80-chromosome G. tabacina. Thus, it is logical to suggest that the 80-chromosome G. tabacina (NAR) is a complex, probably synthesized from A genome (G. canescens, G. clandestina, G. argyrea, G. tomentella D4 isozyme group) and B genome (G. latifolia, G. microphylla, G. tabacina) species, and the 80-chromosome G. tabacina (WAR) complex was evolved through segmental allopolyploidy from the B genome species.Key words: Glycine spp., allopolyploidy, colchicine, genome, intra- and inter-specific hybridization, polyploid complex.

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