scholarly journals Miscanthus: a case study for the utilization of natural genetic variation

2014 ◽  
Vol 13 (3) ◽  
pp. 219-237 ◽  
Author(s):  
T. R. Hodkinson ◽  
M. Klaas ◽  
M. B. Jones ◽  
R. Prickett ◽  
S. Barth
Keyword(s):  
Genetic Variation ◽  
Crop Improvement ◽  
Bioenergy Crops ◽  
F1 Hybrids ◽  
Marginal Lands ◽  
Single Nucleotide ◽  
Natural Genetic Variation ◽  
Trait Locus ◽  
Stressful Environments

Cultivars ofMiscanthusused as bioenergy crops or tested in trials are largely clonally propagated, wild sourced genotypes or clonally propagated F1 hybrids. One of the most productive taxa is the sterile triploidM.× giganteus. Little domestication or breeding has been undertaken and there is huge potential to utilize the extensive genetic resources of the genus for crop improvement. The challenge is to generate new highly adapted genotypes suitable for a range of environments. Production on marginal land, not used for food crops, is particularly desirable, but presents many barriers to crop breeders, as these are largely unproductive and/or stressful environments. This article outlines progress made in characterizing natural genetic variation inMiscanthusincluding next-generation single-nucleotide polymorphism genotyping, quantitative trait locus analysis and association mapping. It also explains how this knowledge is being used to develop novel genotypes suited for growth in a broad range of agricultural and marginal lands by defining breeding pools, generating novel crosses, manipulating polyploidy and applying genomic selection approaches.

scholarly journals Association mapping and genetic dissection of drought-induced canopy temperature differences in rice

2019 ◽  
Vol 71 (4) ◽  
pp. 1614-1627 ◽  
Author(s):  
Giovanni Melandri ◽  
Ankush Prashar ◽  
Susan R McCouch ◽  
Gerard van der Linden ◽  
Hamlyn G Jones ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Grain Yield ◽  
Canopy Temperature ◽  
Leaf Temperature ◽  
Genetic Dissection ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Snp Map ◽  
Trait Locus

Abstract Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering. The canopy temperature of the accessions during stress negatively correlated with grain yield (r= –0.48) and positively with plant height (r=0.56). Temperature values were used to perform a genome-wide association (GWA) analysis using a 45K single nucleotide polynmorphism (SNP) map. A quantitative trait locus (QTL) for canopy temperature under drought was detected on chromosome 3 and fine-mapped using a high-density imputed SNP map. The candidate genes underlying the QTL point towards differences in the regulation of guard cell solute intake for stomatal opening as the possible source of temperature variation. Genetic variation for the significant markers of the QTL was present only within the tall, low-yielding landraces adapted to drought-prone environments. The absence of variation in the shorter genotypes, which showed lower leaf temperature and higher grain yield, suggests that breeding for high grain yield in rice under paddy conditions has reduced genetic variation for stomatal response under drought.

scholarly journals FIND-IT: Ultrafast mining of genome diversity

2021 ◽  
Author(s):  
Soeren Knudsen ◽  
Toni Wendt ◽  
Christoph Dockter ◽  
Hanne Cecilie Thomsen ◽  
Magnus Rasmussen ◽  
...  
Keyword(s):  
Synonymous Codon ◽  
Global Climate ◽  
Crop Improvement ◽  
Digital Pcr ◽  
Rapid Identification ◽  
Single Nucleotide ◽  
Natural Genetic Variation ◽  
Germplasm Collections ◽  
Improvement Methodologies ◽  
Nucleotide Resolution

Novel crop improvement methodologies, including the exploitation of natural genetic variation, are urgently required to feed our rapidly growing human population in the context of global climate change. Here we describe a ‘Fast Identification of Nucleotide variants by DigITal PCR’ (FIND-IT) method for the rapid identification of pre-targeted genetic variants or rare alleles in large genomic populations. Libraries of 500,000 individuals can be screened and desired variants isolated within two weeks. FIND-IT is widely applicable for mining valuable diversity in any genomic population, including elite breeding and wild germplasm collections. The method provides single nucleotide resolution that has been validated by identifying and isolating knockout lines, non-synonymous codon changes and variants of miRNA and transcription factor binding sites in the agronomically important crop barley. In contrast to existing methods, FIND-IT does not require transformation, cloning or enzymatic steps, and is exempt from GMO regulations. Thus, FIND-IT can be applied immediately to elite crop cultivars and can be tailored to minimize or eliminate time-consuming backcrossing requirements.

scholarly journals A framework for genomics-informed ecophysiological modeling in plants

2018 ◽  
Author(s):  
Diane R Wang ◽  
Carmela R Guadagno ◽  
Xiaowei Mao ◽  
D. Scott Mackay ◽  
Jonathan R Pleban ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genomic Prediction ◽  
Large Scale ◽  
Crop Improvement ◽  
Model Development ◽  
Model Performance ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Natural Genetic Variation ◽  
Related Individuals

Dynamic process-based plant models capture complex physiological response across time, carrying the potential to extend simulations out to novel environments and lend mechanistic insight to observed phenotypes. Despite the translational opportunities for varietal crop improvement that could be unlocked by linking natural genetic variation to first-principles based modeling, these models are challenging to apply to large populations of related individuals. Here we use a combination of model development, experimental evaluation, and genomic prediction in Brassica rapa L. to set the stage for future large-scale process-based modeling of intra-specific variation. We develop a new canopy growth sub-model for B. rapa within the process-based model Terrestrial Regional Ecosystem Exchange Simulator (TREES), test input parameters for feasibility of direct estimation with observed phenotypes across cultivated morphotypes and indirect estimation using genomic prediction on a Recombinant Inbred Line population, and explore model performance on an in silico population under non-stressed and mild water stressed conditions. We find evidence that the updated whole plant model has capacity to distill genotype by environment interaction (G x E) into tractable components. The framework presented offers a means to link genetic variation with environment-modulated plant response and serves as a stepping stone towards large-scale prediction of un-phenotyped, genetically-related individuals under un-tested environmental scenarios.

scholarly journals Natural genetic variation affecting transcription factor spacing at regulatory regions is generally well tolerated

2020 ◽  
Author(s):  
Zeyang Shen ◽  
Jenhan Tao ◽  
Gregory J. Fonseca ◽  
Christopher K. Glass
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Binding Sites ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Nucleotide Polymorphisms ◽  
Enhancer Activity ◽  
Single Nucleotide ◽  
Natural Genetic Variation ◽  
Influence Gene Expression

AbstractRegulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Single nucleotide polymorphisms (SNPs) and short insertions and deletions (InDels) can influence gene expression by altering the sequences of TF binding sites. Prior studies also showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of altered TF spacing has not been systematically analyzed in the context of natural genetic variation. Here, we exploit millions of InDels provided by five diverse strains of mice to globally investigate the effects of altered spacing on TF binding and local histone acetylation in macrophages. We find that spacing alterations resulting from InDels are generally well tolerated in comparison to genetic variants that directly alter TF binding sites. These findings have implications for interpretation of non-coding genetic variation and comparative analysis of regulatory elements across species.

scholarly journals Low-temperature-specific effects ofPHYTOCHROME Con the circadian clock in Arabidopsis suggest thatPHYCunderlies natural variation in biological timing

2015 ◽  
Author(s):  
Kieron D Edwards ◽  
Francois Guerineau ◽  
Paul F Devlin ◽  
Andrew J Millar
Keyword(s):  
Genetic Variation ◽  
Circadian Clock ◽  
Red Light ◽  
Circadian System ◽  
Cell Physiology ◽  
Circadian Period ◽  
Functional Variation ◽  
Multiple Sequence ◽  
Natural Genetic Variation ◽  
Trait Locus

The circadian clock is a fundamental feature of gene regulation and cell physiology in eukaryotes and some prokaryotes, and an exemplar gene regulatory network in Systems Biology. The circadian system in Arabidopsis thaliana is complex in part due to its photo-transduction pathways. Analysis of natural genetic variation between Arabidopsis accessions Cape Verde Islands (Cvi-0) and Landsberg erecta (Ler) identified a major, temperature-specific Quantitative Trait Locus (QTL) on chromosome V that altered the circadian period of leaf movement (Edwards et al., Genetics, 2005). We tested Near-Isogenic Lines (NILs) to confirm that Ler alleles at thisPerCv5cQTL lengthened the circadian period at 12°C, with little effect at higher temperatures. ThePHYTOCHROME Cgene lies within the QTL interval, and contains multiple sequence variants. Plants carrying either a T-DNA-insertion intoPHYCor a deletion ofPHYCalso lengthened circadian period under white light, except at 27°C.phyBandphyABEmutants lengthened period only at 12°C. These results extend recent data showing PhyC effects in red light, confirming the number of photoreceptor proteins implicated in the plant circadian system at eleven. The connection between light input mechanisms and temperature effects on the clock is reinforced. Natural genetic variation withinPHYCis likely to underlie thePerCv5cQTL. Our results suggest that functional variation within the PHYC-Ler haplotype group might contribute to the evolution of the circadian system and possibly to clock-related phenotypes such as flowering time. These results have previously passed peer-review, so we provide them in this citable preprint.

Fine mapping of a major QTL controlling early flowering in tomato using QTL-seq

2018 ◽  
Vol 98 (3) ◽  
pp. 672-682 ◽  
Author(s):  
Eaknarin Ruangrak ◽  
Xiaomei Su ◽  
Zejun Huang ◽  
Xiaoxuan Wang ◽  
Yanmei Guo ◽  
...  
Keyword(s):  
Crop Improvement ◽  
Cost Effective ◽  
Physical Region ◽  
Polymerase Chain Reaction Analysis ◽  
Early Flowering ◽  
Chromosome 1 ◽  
Single Nucleotide ◽  
Polymerase Chain ◽  
Trait Locus ◽  
Alignment Analysis

Early flowering is one of the major earliness traits in tomato and is also an important agronomical trait in crop plants; thus, this trait is important for plant breeding and crop improvement. With the innovation of rapid and cost-effective technologies, quantitative trait locus (QTL)-seq has become the preferred method of performing QTL identification. In the present study, we identified a candidate QTL of an early flowering trait in tomato (Solanum lycopersicum) using QTL-seq. Two DNA pools of the extreme phenotype of the F2 progeny from crosses between the ‘Bone MM’ cultivar (early flowering, P1) and ‘071-440’ cultivar (late flowering, P2) were bulked for sequencing and an alignment analysis. We observed 220 single nucleotide polymorphism markers, seven candidate QTLs, and genes that may be associated with early flowering located between 1.6 and 71.8 Mb on chromosome 1. Using traditional QTL analysis, the location of one QTL was confirmed in the physical region between 23.5 and 25.3 Mb, which corresponded to the region identified using QTL-seq, and was referred to as EF1 (Solyc01g017060). A real-time quantitative reverse transcription polymerase chain reaction analysis showed that EF1 was the most highly expressed among the candidate genes and significantly expressed in early flowering parents and furthermore, we found that EF1, which had a similar sequence to the Ycf2 gene, may relate to the early flowering phenotype.

Implementing molecular marker technology in forage improvement

2003 ◽  
pp. 229-238
Author(s):  
M. Faville ◽  
B. Barrett ◽  
A. Griffiths ◽  
M. Schreiber ◽  
C. Mercer ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Genetic Variation ◽  
White Clover ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Seedling Vigour ◽  
Genome Map ◽  
Trait Locus ◽  
Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

scholarly journals Genetic Diversity of Landraces and Improved Varieties of Rice (Oryza sativa L.) in Taiwan

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ai-ling Hour ◽  
Wei-hsun Hsieh ◽  
Su-huang Chang ◽  
Yong-pei Wu ◽  
Han-shiuan Chin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Indigenous Peoples ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Genetic Erosion ◽  
Germplasm Conservation ◽  
Gene Pools ◽  
Improved Varieties ◽  
Breeding Goals

Abstract Background Rice, the most important crop in Asia, has been cultivated in Taiwan for more than 5000 years. The landraces preserved by indigenous peoples and brought by immigrants from China hundreds of years ago exhibit large variation in morphology, implying that they comprise rich genetic resources. Breeding goals according to the preferences of farmers, consumers and government policies also alter gene pools and genetic diversity of improved varieties. To unveil how genetic diversity is affected by natural, farmers’, and breeders’ selections is crucial for germplasm conservation and crop improvement. Results A diversity panel of 148 rice accessions, including 47 cultivars and 59 landraces from Taiwan and 42 accessions from other countries, were genotyped by using 75 molecular markers that revealed an average of 12.7 alleles per locus with mean polymorphism information content of 0.72. These accessions could be grouped into five subpopulations corresponding to wild rice, japonica landraces, indica landraces, indica cultivars, and japonica cultivars. The genetic diversity within subpopulations was: wild rices > landraces > cultivars; and indica rice > japonica rice. Despite having less variation among cultivars, japonica landraces had greater genetic variation than indica landraces because the majority of Taiwanese japonica landraces preserved by indigenous peoples were classified as tropical japonica. Two major clusters of indica landraces were formed by phylogenetic analysis, in accordance with immigration from two origins. Genetic erosion had occurred in later japonica varieties due to a narrow selection of germplasm being incorporated into breeding programs for premium grain quality. Genetic differentiation between early and late cultivars was significant in japonica (FST = 0.3751) but not in indica (FST = 0.0045), indicating effects of different breeding goals on modern germplasm. Indigenous landraces with unique intermediate and admixed genetic backgrounds were untapped, representing valuable resources for rice breeding. Conclusions The genetic diversity of improved rice varieties has been substantially shaped by breeding goals, leading to differentiation between indica and japonica cultivars. Taiwanese landraces with different origins possess various and unique genetic backgrounds. Taiwanese rice germplasm provides diverse genetic variation for association mapping to unveil useful genes and is a precious genetic reservoir for rice improvement.

scholarly journals Genomic Analyses of Globodera pallida, A Quarantine Agricultural Pathogen in Idaho

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 363
Author(s):  
Sulochana K. Wasala ◽  
Dana K. Howe ◽  
Louise-Marie Dandurand ◽  
Inga A. Zasada ◽  
Dee R. Denver
Keyword(s):  
Genetic Variation ◽  
Potato Production ◽  
Globodera Pallida ◽  
Fixation Index ◽  
Parasitic Nematodes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Field Samples ◽  
Multiple Introduction

Globodera pallida is among the most significant plant-parasitic nematodes worldwide, causing major damage to potato production. Since it was discovered in Idaho in 2006, eradication efforts have aimed to contain and eradicate G. pallida through phytosanitary action and soil fumigation. In this study, we investigated genome-wide patterns of G. pallida genetic variation across Idaho fields to evaluate whether the infestation resulted from a single or multiple introduction(s) and to investigate potential evolutionary responses since the time of infestation. A total of 53 G. pallida samples (~1,042,000 individuals) were collected and analyzed, representing five different fields in Idaho, a greenhouse population, and a field in Scotland that was used for external comparison. According to genome-wide allele frequency and fixation index (Fst) analyses, most of the genetic variation was shared among the G. pallida populations in Idaho fields pre-fumigation, indicating that the infestation likely resulted from a single introduction. Temporal patterns of genome-wide polymorphisms involving (1) pre-fumigation field samples collected in 2007 and 2014 and (2) pre- and post-fumigation samples revealed nucleotide variants (SNPs, single-nucleotide polymorphisms) with significantly differentiated allele frequencies indicating genetic differentiation. This study provides insights into the genetic origins and adaptive potential of G. pallida invading new environments.

Sign in / Sign up

Export Citation Format

Share Document