Summary of the polymorphic markers integrated in to the 21 chromosomes based on 158 recombinant inbred lines derived from a cross between two spring wheat cultivars, ‘Cutler’ x ‘AC Barrie’.

<p>Chromosome 2A, 3A, 3B, 5A and 7B each has two linkage groups.</p

Summary of the QTLs associated with flowering time, maturity, plant height and grain yield on 158 recombinant inbred lines derived from a cross between spring wheat cultivars, ‘Cutler’ and ‘AC Barrie’.

<p>The results are for the combined two environments for flowering time under greenhouse and five environments for flowering time, maturity, plant height and grain yield under field conditions.</p

Frequency distribution of least square means computed from the combined data of five environments.

<p>The arrows indicate values of the two parents (C = Cutler; A = AC Barrie). ‘Cutler’ flowered and matured 2.6 days earlier, 12.9 cm shorter but produced 154.9 kg ha^-1 lower grain yield than ‘AC Barrie’.</p

Observed frequency distribution of linkage map distances between adjacent loci based on the 1811 markers mapped to the 21 hexaploid wheat chromosomes.

<p>Observed frequency distribution of linkage map distances between adjacent loci based on the 1811 markers mapped to the 21 hexaploid wheat chromosomes.</p

Linkage map of the 10 wheat chromosomes that have at least one QTL associated with flowering time, maturity, plant height and/or grain yield.

<p>Map position in centiMorgans (cM) is shown on the left side of the chromosomes, with each horizontal line representing a marker. QTLs names are shown on the right side of each linkage group, with bars indicating their confidence interval. QTLs for flowering, maturity, plant height and grain yield are in black, red, pink and green font, respectively. QTLs for flowering time under greenhouse have NDG-06, NDG-08 and NDG-com after chromosome number, which refers to the trials in 2006, 2008 and combined, respectively. QTLs for both flowering and maturity under field conditions have either NDF or DDF, which refers to number of days under field and degree days under field, respectively, followed by 07, 08E (early plating), 08L (late planting), 11, 12 or com after chromosome, which indicate the last two digits of the corresponding year of the trials or combined data of all trials. QTLs for pant height and grain yield have the last two digits of the trial year or com for combined. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160623#pone.0160623.s003" target="_blank">S3 Table</a> for details.</p

MeioCapture: an efficient method for staging and isolation of meiocytes in the prophase I sub-stages of meiosis in wheat

Background Molecular analysis of meiosis has been hindered by difficulties in isolating high purity subpopulations of sporogenous cells representing the succeeding stages of meiosis. Isolation of purified male meiocytes from defined meiotic stages is crucial in discovering meiosis specific genes and associated regulatory networks. Results We describe an optimized method termed MeioCapture for simultaneous isolation of uncontaminated male meiocytes from wheat (Triticum spp.), specifically from the pre-meiotic G2 and the five sub-stages of meiotic prophase I. The MeioCapture protocol builds on the traditional anther squash technique and the capillary collection method, and involves extrusion of intact sporogenous archesporial columns (SACs) containing meiocytes. This improved method exploits the natural meiotic synchrony between anthers of the same floret, the correlation between the length of anthers and meiotic stage, and the occurrence of meiocytes in intact SACs largely free of somatic cells. The main advantage of MeioCapture, compared to previous methods, is that it allows simultaneous collection of meiocytes from different sub-stages of prophase I at a very high level of purity, through correlation of stages with anther sizes. A detailed description is provided for all steps, including the collection of tissue, isolation and size sorting of anthers, extrusion of intact SACs, and staging of meiocytes. Precautions for individual steps throughout the procedure are also provided to facilitate efficient isolation of pure meiocytes. The proof-of-concept was successfully established in wheat, and a light microscopic atlas of meiosis, encompassing all stages from pre-meiosis to telophase II, was developed. Conclusion The MeioCapture method provides an essential technique to study the molecular basis of chromosome pairing and exchange of genetic information in wheat, leading to strategies for manipulating meiotic recombination frequencies. The method also provides a foundation for similar studies in other crop species

Comparisons of recombinant inbred lines that had the ‘CDC Go’ or ‘Attila’ alleles at the flanking markers of three coincident QTLs on eight traits evaluated under seven (2008–2014) conventional management environments.

<p>RILs with recombinant genotypes at the flanking markers of each coincident QTL were excluded from analysis.</p

The distribution of QTLs associated with eight agronomic traits evaluated across three (2008–2010) organically managed environments (blue font) and seven (2008–2014) conventionally managed environments (pink font).

<p>Map position in centiMorgans (cM) is shown on the left side of the chromosomes, with each horizontal line representing a marker. QTLs are shown on the right side of each linkage group, with bars indicating their 95% genetic confidence interval. Details of each QTL under conventional management is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171528#pone.0171528.t003" target="_blank">Table 3</a>, while those QTLs under organic management is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171528#pone.0171528.s003" target="_blank">S2 Table</a>.</p

Comparisons of QTLs associated with eight agronomic traits in our previous study [9] and present study.

<p>The previous study was based on averaged phenotypic data of three (2008–2010) conventionally managed environments and genotypic data of 579 DArT and the <i>Rht-B1</i> gene specific markers, while the present study was based seven environments (2008–2014) and 1203 SNP and gene specific markers.</p

Summary of QTLs associated with the different traits based on 167 recombinant inbred line (RIL) population evaluated at seven environments from 2008 to 2014 under conventional management system.

<p>QTL analyses were conducted using least squares means of each environment and averaged (combined) across all seven environments.</p