No abstract

To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in crop breeding. One way this can be achieved is through 'speed breeding' (SB), which shortens the breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plant's daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.

Polyploidy complicates genomics-based breeding of many crops, including wheat, potato, cotton, oat and sugarcane. To address this challenge, we sequenced leaf transcriptomes across a mapping population of the polyploid crop oilseed rape (Brassica napus) and representative ancestors of the parents of the population. Analysis of sequence variation and transcript abundance enabled us to construct twin single nucleotide polymorphism linkage maps of B. napus, comprising 23,037 markers. We used these to align the B. napus genome with that of a related species, Arabidopsis thaliana, and to genome sequence assemblies of its progenitor species, Brassica rapa and Brassica oleracea. We also developed methods to detect genome rearrangements and track inheritance of genomic segments, including the outcome of an interspecific cross. By revealing the genetic consequences of breeding, cost-effective, high-resolution dissection of crop genomes by transcriptome sequencing will increase the efficiency of predictive breeding even in the absence of a complete genome sequence.

10To meet the challenge of feeding a growing population, breeders and scientists are continuously 11 looking for ways to increase genetic gain in crop breeding. One way this can be achieved is through 12'speed breeding' (SB), which shortens the breeding cycle and accelerates research studies through

We constructed a linkage map for the population QDH, which was derived from a cross between an oilseed rape cultivar and a resynthesised Brassica napus. The linkage map included ten markers linked to loci orthologous to those encoding fatty acid biosynthesis genes in Arabidopsis thaliana. The QDH population contains a high level of allelic variation, particularly in the C genome. We conducted quantitative trait locus (QTL) analyses, using field data obtained over 3 years, for the fatty acid composition of seed oil. The population segregates for the two major loci controlling erucic acid content, on linkage groups A8 and C3, which quantitatively affect the content of other fatty acids and is a problem generally encountered when crossing "wild" germplasm with cultivated "double low" oilseed rape cultivars. We assessed three methods for QTL analysis, interval mapping, multiple QTL mapping and single marker regression analysis of the subset of lines with low erucic acid. We found the third of these methods to be most appropriate for our main purpose, which was the study of the genetic control of the desaturation of 18-carbon fatty acids. This method enabled us to decouple the effect of the segregation of the erucic acid-controlling loci and identify 34 QTL for fatty acid content of seed oil, 14 in the A genome and 20 in the C genome. The QTL indicate the presence of 13 loci with novel alleles inherited from the progenitors of the resynthesised B. napus that might be useful for modulating the content or extent of desaturation of polyunsaturated fatty acids, only one of which coincides with the anticipated position of a candidate gene, an orthologue of FAD2.

Water use efficiency (WUE) is an important trait that has been associated with drought tolerance of crop plants, and leaf ash (LASH) generally related to WUE. A restriction fragment length polymorphism (RFLP) map was constructed from a soybean [Glycine max (L.) Merr.] population of 120 F4-derived lines from a cross of'Young' × P1416937. The purpose of this research was to identify quantitative trait loci (QTL) associated with WUE and LASH in 36-d-old, greenhouse-grown plants. The experimental design was a randomized complete block with six replications. Significant (P < 0.01) phenotypic differences were detected among the lines for both traits. A total of four and six independent RFLP markers were associated with WUE and LASH and if combined each group of markers would explain 38 and 53% of the variability in the respective traits. One marker locus (cr497-1), on USDA Linkage Group J, explained 13.2% of the variation in WUE indicating the presence of a major QTL. The LASH was negatively correlated with WUE (r = -0.40"*), and two QTL were associated with both WUE and LASH. For each of these QTL, the allele for increased WUE was associated with reduced LASH.

Many important plant species have polyploidy in their recent ancestry, complicating inferences about the genetic basis of trait variation. Although the principal locus controlling the proportion of polyunsaturated fatty acids (PUFAs) in seeds of Arabidopsis thaliana is known (fatty acid desaturase 2; FAD2), commercial cultivars of a related crop, oilseed rape (Brassica napus), with very low PUFA content have yet to be developed. We showed that a cultivar of oilseed rape with lower than usual PUFA content has non-functional alleles at three of the four orthologous FAD2 loci. To explore the genetic basis further, we developed an ethyl methanesulphonate mutagenised population, JBnaCAB_E, and used it to identify lines that also carried mutations in the remaining functional copy. This confirmed the hypothesised basis of variation, resulting in an allelic series of mutant lines showing a spectrum of PUFA contents of seed oil. Several lines had PUFA content of ~6 % and oleic acid content of ~84 %, achieving a long-standing industry objective: very high oleic, very low PUFA rapeseed without the use of genetic modification technology. The population contains a high rate of mutations and represents an important resource for research in B. napus.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-013-9954-5) contains supplementary material, which is available to authorized users.

SummaryPlants with winter annual life history germinate in summer or autumn and require a period of prolonged winter cold to initiate flowering, known as vernalization. In the Brassicaceae, the requirement for vernalization is conferred by high expression of orthologs of the FLOWERING LOCUS C (FLC) gene, the expression of which is known to be silenced by prolonged exposure to winter-like temperatures [1]. Based on a wealth of vernalization experiments, typically carried out in the range of 5°C–10°C, we would expect field environments during winter to induce flowering in crops with winter annual life history. Here, we show that, in the case of winter oilseed rape, expression of multiple FLC orthologs declines not during winter but predominantly during October when the average air temperature is 10°C–15°C. We further demonstrate that plants proceed through the floral transition in early November and overwinter as inflorescence meristems, which complete floral development in spring. To validate the importance of pre-winter temperatures in flowering time control, we artificially simulated climate warming in field trial plots in October. We found that increasing the temperature by 5°C in October results in raised FLC expression and delays the floral transition by 3 weeks but only has a mild effect on flowering date the following spring. Our work shows that winter annuals overwinter as a floral bud in a manner that resembles perennials and highlights the importance of studying signaling events in the field for understanding how plants transition to flowering under real environmental conditions.