Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Few genetic markers, if any, have found such widespread use as microsatellites, or simple/short tandem repeats. Features such as hypervariability and ubiquitous occurrence explain their usefulness, but these features also pose several questions. For example, why are microsatellites so abundant, why are they so polymorphic and by what mechanism do they mutate? Most importantly, what governs the intricate balance between the frequent genesis and expansion of simple repetitive arrays, and the fact that microsatellite repeats rarely reach appreciable lengths? In other words, how do microsatellites evolve?

/pdf/microsatellites-simple-sequences-with-complex-evolution-5by92lfg3w.pdf

Microsatellites: simple sequences with complex evolution

A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley (Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3′-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5′-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 ± 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.

Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.).

This review describes physiological mechanisms and selectable indicators of gene action, with the aim of promoting new screening methods to identify genetic variation for increasing the salt tolerance of cereal crops. Physiological mechanisms that underlie traits for salt tolerance could be used to identify new genetic sources of salt tolerance. Important mechanisms of tolerance involve Na+ exclusion from the transpiration stream, sequestration of Na+ and Cl- in the vacuoles of root and leaf cells, and other processes that promote fast growth despite the osmotic stress of the salt outside the roots. Screening methods for these traits are discussed in relation to their use in breeding, particularly with respect to wheat. Precise phenotyping is the key to finding and introducing new genes for salt tolerance into crop plants.

Approaches to increasing the salt tolerance of wheat and other cereals

https://www.cell.com/trends/biotechnology/pdf/S0167-7799(04)00322-1.pdf

Genic microsatellite markers in plants: features and applications

We quantified grain sodium (Na+) content across a barley GWAS panel grown under optimal conditions. We identified a strong association with a region containing two low and one high Na+ accumulating haplotypes of a Class 1 HIGH-AFFINITY POTASSIUM TRANSPORTER (HKT1;5) known to be involved in regulating plant Na+ homeostasis. The haplotypes exhibited an average 1.8-fold difference in grain Na+ content. We show that an L189P substitution disrupts Na+ transport in the high Na+ lines, disturbs the plasma membrane localisation typical of HKT1;5 and induces a conformational change in the protein predicted to compromise function. Under NaCl stress, lines containing P189 accumulate high levels of Na+, but show no significant difference in biomass. P189 increases in frequency from wild-species to elite cultivars leading us to speculate that the compromised haplotype is undergoing directional selection possibly due to the value of Na+ as a functional nutrient in non-saline environments.

https://www.biorxiv.org/content/biorxiv/early/2020/01/23/2020.01.23.916742.full.pdf

A Grain of Salt

Genetic control of infection and symptom expression by Rhynchosporium commune in barley.

Waterlogging is a major factor limiting barley grain yield worldwide. Climate change will likely increase this water stress in Northern Europe. Breeding for waterlogging tolerance (WLT), as for other abiotic stresses, is difficult, but identification of genetic markers linked to genes affecting WLT could facilitate the breeding process. To identify a suitable marker population, parents of 14 double-haploid (DH) barley populations were tested for segregation of biomass growth reduction in waterlogged soil. The most interesting was found in the offspring from crossing cv. Psaknon and breeding line

/pdf/qtl-for-chlorophyll-fluorescence-of-barley-plants-grown-at-269djrsq5l.pdf

QTL for chlorophyll fluorescence of barley plants grown at low oxygen concentration in hydroponics to simulate

Programmed meiotic DNA double-strand breaks (DSBs), necessary for proper chromosomal segregation and viable gamete formation, are repaired by homologous recombination (HR) as crossovers (COs) or non-crossovers (NCOs). The mechanisms regulating the number and distribution of COs are still poorly understood. The regulator of telomere elongation helicase 1 (RTEL1) DNA helicase was previously shown to enforce the number of meiotic COs in Caenorhabditis elegans but its function in plants has been studied only in the vegetative phase. Here, we characterised barley RTEL1 gene structure and expression using RNA-seq data previously obtained from vegetative and reproductive organs and tissues. Using RNAi, we downregulated RTEL1 expression specifically in reproductive tissues and analysed its impact on recombination using a barley 50k iSelect SNP Array. Unlike in C. elegans, in a population segregating for RTEL1 downregulated by RNAi, high resolution genome-wide genetic analysis revealed a significant increase of COs at distal chromosomal regions of barley without a change in their total number. Our data reveal the important role of RTEL1 helicase in plant meiosis and control of recombination.

/pdf/downregulation-of-barley-regulator-of-telomere-elongation-58duub9ecp.pdf

Downregulation of Barley Regulator of Telomere Elongation Helicase 1 Alters the Distribution of Meiotic Crossovers.

This paper describes the genetic control of two new water-soluble proteins in barley. Water-soluble proteins (WSPs) of mature barley seed form part of the albumin/globulin class of seed proteins. They can be extracted from hand-milled grain with water, though some WSPs are more efficiently extracted with a solution of 10 mM dithiothreitol. Polymorphisms for WSPs were detected in isoelectric focusing gels incorporating various ampholine combinations. Two new controlling genes (Wsp4 andWsp5) have been identified and located using wheat/barley chromosome addition lines and barley doubled haploids.Wsp4 is located on chromosome 2 (2H), andWsp5 was found to be tightly linked toWsp2 on the long arm of chromosome 7 (5HL). Segregation of a sixth gene (Wsp6) is also described, but this has not been mapped. The results are discussed with respect to other previously mappedWsp loci.

Malcolm Macaulay

Papers

A Grain of Salt

Genetic control of infection and symptom expression by Rhynchosporium commune in barley.

QTL for chlorophyll fluorescence of barley plants grown at low oxygen concentration in hydroponics to simulate

Downregulation of Barley Regulator of Telomere Elongation Helicase 1 Alters the Distribution of Meiotic Crossovers.

Extraction and Genetic Control of Two New Water-Soluble Proteins of Mature Barley Seed