Explore the vast range of titles available.

Wheat yield is highly correlated with plant height, heading date, spike characteristics, and kernel traits. In this study, we used the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line population of 165 lines constructed by crossing two tetraploid wheat materials, Icaro and Y4. A genetic linkage map with a total length of 6244.51 cM was constructed, covering 14 chromosomes of tetraploid wheat. QTLs for 12 important agronomic traits, including plant height (PH), heading date (HD), awn color (AC), spike-branching (SB), and related traits of spike and kernel, were mapped in multiple environments, while combined QTL-by-environment interactions and epistatic effects were analyzed for each trait. A total of 52 major or stable QTLs were identified, among which may be some novel loci controlling PH, SB, and kernel length-width ratio (LWR), etc., with LOD values ranging from 2.51 to 54.49, thereby explaining 2.40–66.27% of the phenotypic variation. Based on the ‘China Spring’ and durum wheat reference genome annotations, candidate genes were predicted for four stable QTLs, QPH.nwafu-2B.2 (165.67–166.99 cM), QAC.nwafu-3A.1 (419.89–420.52 cM), QAC.nwafu-4A.1 (424.31–447.4 cM), and QLWR.nwafu-7A.1 (166.66–175.46 cM). Thirty-one QTL clusters and 44 segregation distortion regions were also detected, and 38 and 18 major or stable QTLs were included in these clusters and segregation distortion regions, respectively. These results provide QTLs with breeding application potential in tetraploid wheat that broadens the genetic basis of important agronomic traits such as PH, HD, AC, SB, etc., and benefits wheat breeding.

Segregation distortion can negatively impact on gains expected using selection. In order to increase our understanding of genetic factors that may influence the extent and direction of segregation distortion, segregation distortion analyses were conducted in four different doubled haploid (DH) populations. A high-density composite map of barley was then constructed by integrating information from the four populations. The composite map contained 2,111 unique loci, comprising RFLP, SSR and DArT markers and spanned 1,136 cM. In the four populations investigated, the proportion of markers with segregation distortion ranged from 15 to 38%, depending on the population. The highest distortion was observed in populations derived by the microspore culture technique. Distorted loci tended to be clustered, which allowed definition of segregation distortion regions (SDRs). A total of 14 SDRs were identified in the 4 populations. Using the high-density composite map, several SDRs were shown to have consistent map locations in two or more populations; one SDR on chromosome 1H was present in all four populations. The analysis of haplotypes underlying seven SDRs indicated that in three cases the under-represented haplotypes were common across populations, but for four SDRs the under-represented haplotypes varied across populations. Six of the seven centromeric regions harboured SDRs suggesting that genetic processes related to position near a centromere caused the segregation distortion in these SDRs. Other SDRs were most likely due to the methods used to produce the DH populations. The association of the SDRs identified in this study and some of the genes involved in the process of haploid production described in other studies were compared. The composite map constructed in this study provides an additional resource for the barley community via increased genome coverage and the provision of additional marker options. It has also enabled further insights into mechanisms that underpin segregation distortion.

Meiotically driving sex chromosomes manipulate gametogenesis to increase their transmission at a cost to the rest of the genome. The intragenomic conflicts they produce have major impacts on the ecology and evolution of their host species. However, their ecological dynamics remain poorly understood. Simple population genetic models predict meiotic drivers will rapidly reach fixation in populations and spread across landscapes. In contrast, natural populations commonly show spatial variation in the frequency of drivers, with drive present in clines or mosaics across species ranges. For example, Drosophila subobscura harbors a sex ratio distorting drive chromosome (SRs) at 15–25% frequency in North Africa, present at less than 2% frequency in adjacent southern Spain, and absent in other European populations. Here, we investigate the forces preventing the spread of the driver northward. We show that SRs has remained at a constant frequency in North Africa, and failed to spread in Spain. We find strong evidence that spread is impeded by genetic incompatibility between SRs and Spanish autosomal backgrounds. When we cross SRs from North Africa onto Spanish genetic backgrounds we observe strong incompatibilities specific to hybrids bearing SRs. The incompatibilities increase in severity in F2 male hybrids, leading to almost complete infertility. We find no evidence supporting an alternative hypothesis, that there is resistance to drive in Spanish populations. We conclude that the source of the stepped frequency variation is genetic incompatibility between the SRs chromosome and the genetic backgrounds of the adjacent population, preventing SRs spreading northward. The low frequency of SRs in South Spain is consistent with recurrent gene flow across the Strait of Gibraltar combined with selection against the SRs element through genetic incompatibility. This demonstrates that incompatibilities between drive chromosomes and naïve populations can prevent the spread of drive between populations, at a continental scale.

Marker segregation distortion is a common natural phenomenon. However, relatively little is known about utilizing distorted markers for detecting quantitative trait loci (QTL). Therefore, in this study we proposed a multi-QTL mapping approach that uses distorted markers. First, the information from all markers, including distorted markers, was used to detect segregation distortion loci (SDL). Second, the information from the detected SDL was used to correct the conditional probabilities of the QTL genotypes conditional on marker information, and these corrected probabilities were then incorporated into a multi-QTL mapping methodology. Finally, the proposed approach was validated by both Monte Carlo simulation studies and real data analysis. The results from the simulation studies show that as long as one or two SDL are placed around the simulated QTL, there are no differences between the new method and the ordinary interval mapping method in terms of the power of QTL detection or the estimates of the position and dominant effects of the QTL. However, the power of QTL detection is higher under the dominant genetic model of SDL than under the additive genetic model, and the estimate for the additive effect of QTL using the new method is significantly different from the estimate obtained using ordinary interval mapping. The above results were further confirmed by the detection of QTL for dried soymilk in 222 F₂:₄ families in soybean.

Genotyping by sequencing (GBS) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. Unlike other high-density genotyping technologies which have mainly been applied to general interest “reference” genomes, the low cost of GBS makes it an attractive means of saturating mapping and breeding populations with a high density of SNP markers. One barrier to the widespread use of GBS has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous SNP calls which are not easily diagnosed or corrected. In this study, we use a 384-plex GBS protocol to add 30,984 markers to an indica (IR64) × japonica (Azucena) mapping population consisting of 176 recombinant inbred lines of rice (Oryza sativa) and we release our imputation and error correction pipeline to address initial GBS data sparsity and error, and streamline the process of adding SNPs to RIL populations. Using the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. We mapped QTL for leaf width and aluminum tolerance, and were able to identify additional QTL for both phenotypes when using the full set of 30,984 SNPs that were not identified using a subset of only 1,464 SNPs, including a previously unreported QTL for aluminum tolerance located directly within a recombination hotspot on chromosome 1. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.

Understanding the genomic complexity of bread wheat is important for unraveling domestication processes, environmental adaptation, and for future of... Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focusing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating biparental populations was developed, mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity. A modern spring elite variety, “Paragon,” was used as common reference parent. Genetic maps were constructed following identical rules to make them comparable. In total, 1611 linkage groups were identified, based on recombination from an estimated 126,300 crossover events over the whole NAM panel. A consensus map, named landrace consensus map (LRC), was constructed and contained 2498 genetic loci. These newly developed genetics tools were used to investigate the rules underlying genome fluidity or rigidity, e.g., by comparing marker distances and marker orders. In general, marker order was highly correlated, which provides support for strong synteny between bread wheat accessions. However, many exceptional cases of incongruent linkage groups and increased marker distances were also found. Segregation distortion was detected for many markers, sometimes as hot spots present in different populations. Furthermore, evidence for translocations in at least 36 of the maps was found. These translocations fell, in general, into many different translocation classes, but a few translocation classes were found in several accessions, the most frequent one being the well-known T5B:7B translocation. Loci involved in recombination rate, which is an interesting trait for plant breeding, were identified by QTL analyses using the crossover counts as a trait. In total, 114 significant QTL were detected, nearly half of them with increasing effect from the nonreference parents.

Several options are available to the scientific community for genetic map construction but few are simple to install and use. Available programs either lack intuitive interface or are commercial, expensive for many laboratories. We present MapDisto, a free, user-friendly and powerful program for constructing genetic maps from experimental segregating populations. MapDisto is freely available at http://mapdisto.free.fr/DL/ . Current version: 1.7.5.

Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.

Background Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers. Results Three RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes ( Sr58 / Lr46 / Yr29 , Sr2 / Yr30 / Lr27 , and Sr57 / Lr34 / Yr18 ) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence. Conclusion The consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding.

Key message QTL analysis revealed two interacting loci, FS1.2 and FS2.1, underlying round fruit shape in WI7239 cucumber; CsSUN , a homolog of tomato fruit shape gene SUN , was a candidate for FS1.2 . Fruit size is an important quality and yield trait in cucumber, but its genetic basis remains poorly understood. Here we reported QTL mapping results on fruit size with segregating populations derived from the cross between WI7238 (long fruit) and WI7239 (round fruit) inbred cucumber lines. Phenotypic data of fruit length and diameter were collected at anthesis, immature and mature fruit stages in four environments. Ten major-effect QTL were detected for six traits; synthesis of information from these QTL supported two genes, FS1.2 and FS2.1, underlying fruit size variation in the examined populations. Under the two-gene model, deviation from expected segregation ratio in fruit length and diameter among segregating populations was observed, which could be explained mainly by the interactions between FS1.2 and FS2.1 , and segregation distortion in the FS2.1 region. Genome-wide candidate gene search identified CsSUN , a homolog of the tomato fruit shape gene SUN , as the candidate for FS1.2 . The round-fruited WI7239 had a 161-bp deletion in the first exon of CsSUN , and its expression in WI7239 was significantly lower than that in WI7238. A marker derived from this deletion was mapped at the peak location of FS1.2 in QTL analysis. Comparative analysis suggested the melon gene CmSUN - 14 , a homolog of CsSUN as a candidate of the fl2/fd2/fw2 QTL in melon. This study revealed the unique genetic architecture of round fruit shape in WI7239 cucumber. It also highlights the power of QTL analysis for traits with a simple genetic basis but their expression is complicated by other factors.