Genome-wide mapping and prediction suggests presence of local epistasis in a vast elite winter wheat populations adapted to Central Europe

Key message

Genome-wide association mapping as well as marker- and haplotype-based genome-wide selection unraveled a complex genetic architecture of grain yield with absence of large effect QTL and presence of local epistatic effects.

Abstract

The genetic architecture of grain yield determines to a large extent the optimum design of genomic-assisted wheat breeding programs. The main goal of our study was to examine the potential and limitations to dissect the genetic architecture of grain yield in wheat using a large experimental data set. Our study was based on phenotypic information and genomic data of 13,901 SNPs of a diverse set of 3816 elite wheat lines adapted to Central Europe. We applied genome-wide association mapping based on experimental and simulated data sets and performed marker- and haplotype-based genomic prediction. Computer simulations revealed for our mapping population a high power to detect QTL, even if they individually explained only 2.5% of the genetic variation. Despite this, we found no stable marker–trait associations when validating in independent subsets. A two-dimensional scan for marker–marker interactions indicated presence of local epistasis which was further supported by improved prediction abilities when shifting from marker- to haplotype-based genome-wide prediction approaches. We observed that marker effects estimated using genome-wide prediction approaches strongly varied across years albeit resulting in high prediction abilities. Thus, our results suggested that the prediction accuracy of genomic selection in wheat is mainly driven by relatedness rather than by exploiting knowledge of the genetic architecture.

     

A consensus map of rye integrating mapping data from five mapping populations

A consensus map of rye (Secale cereale L.) was constructed using JoinMap 2.0 based on mapping data from five different mapping populations, including ‘UC90’ × ‘E-line’, ‘P87’ × ‘P105’, ‘I_0.1-line’ × ‘I_0.1-line’, ‘E-line’ × ‘R-line’, and ‘Ds2’ × ‘RxL10’. The integration of the five mapping populations resulted in a 779-cM map containing 501 markers with the number of markers per chromosome ranging from 57 on 1R to 86 on 4R. The linkage sizes ranged from 71.5 cM on 2R to 148.7 cM on 4R. A comparison of the individual maps to the consensus map revealed that the linear locus order was generally in good agreement between the various populations, but the 4R orientations were not consistent among the five individual maps. The 4R short arm and long arm assignments were switched between the two population maps involving the ‘E-line’ parent and the other three individual maps. Map comparisons also indicated that marker order variations exist among the five individual maps. However, the chromosome 5R showed very little marker order variation among the five maps. The consensus map not only integrated the linkage data from different maps, but also greatly increased the map resolution, thus, facilitating molecular breeding activities involving rye and triticale.     

Genetic and physical mapping of homoeologous recombination points involving wheat chromosome 2B and rye chromosome 2R.

Wide hybrids have been used in generating genetic maps of many plant species. In this study, genetic and physical mapping was performed on ph1b-induced recombinants of rye chromosome 2R in wheat (Triticum aestivum L.). All recombinants were single breakpoint translocations. Recombination 2RS-2BS was absent from the terminal and the pericentric regions and was distributed randomly along an intercalary segment covering approximately 65% of the arm's length. Such a distribution probably resulted from structural differences at the telomeres of 2RS and wheat 2BS arm that disrupted telomeric initiation of pairing. Recombination 2RL-2BL was confined to the terminal 25% of the arm's length. A genetic map of homoeologous recombination 2R-2B was generated using relative recombination frequencies and aligned with maps of chromosomes 2B and 2R based on homologous recombination. The alignment of the short arms showed a shift of homoeologous recombination toward the centromere. On the long arms, the distribution of homoeologous recombination was the same as that of homologous recombination in the distal halves of the maps, but the absence of multiple crossovers in homoeologous recombination eliminated the proximal half of the map. The results confirm that homoeologous recombination in wheat is based on single exchanges per arm, indicate that the distribution of these single homoeologous exchanges is similar to the distribution of the first (distal) crossovers in homologues, and suggest that successive crossovers in an arm generate specific portions of genetic maps. A difference in the distribution of recombination between the short and long arms indicates that the distal crossover localization in wheat is not dictated by a restricted distribution of DNA sequences capable of recombination but by the pattern of pairing initiation, and that can be affected by structural differences. Restriction of homoeologous recombination to single crossovers in the distal part of the genetic map complicates chromosome engineering efforts targeting genes in the proximal map regions.     

Molecular mapping of two dwarfing genes differing in their GA response on chromosome 2H of barley

The two recessive dwarfing mutants gai (GA-ins) and gal (GA-less), differing in their response to exogenously applied gibberellic acid (GA₃), were mapped in the centromere region and on the long arm, respectively, of the barley chromosome 2H. The gene gai, which determines reduced plant height and GA insensitivity pleiotropically, was found to co-segregate with the two RFLP markers Xmwg2058 and Xmwg2287. Both markers are known to map close to the centromere. The GA-sensitive dwarfing gene gal was found to be linked to the three co-segregating RFLP markers Xmwg581, Xmwg882 and Xmwg2212 (proximal) and XksuG5 (distal) by 3.6 and 9.5. cM, respectively. The distance between the two mutant loci was estimated to be about 55 cM. Homoeologous relationships between the dwarfing genes within the Triticeae are discussed. Received: 11 December 1998 / Accepted: 11 February 1999     

Linkage mapping of mutant loci in rye (Secale cereale L.)

Eight mutant loci determining the traits waxy plant (w and wa1), brown culm (cb), multiple pistils (mp), weak plant with reduced plant height (np), monoculm growth habit (mc), compactum growth habit (ct3) and anthocyaninless (an) were mapped on rye chromosomes 4R (w, np), 6R (cb, mc) and 7R (mp, wa1, ct3, an). For five mutants (w, wa1, cb, mp, np) molecular and biochemical markers were applied, whereas for mc, ct3 and an a classical linkage analysis was performed. Furthermore, it could be demonstrated that homoeologous relationships exist between most of the mapped rye loci and comparable mutants in wheat and barley. It was confirmed not only that genes controlling fundamental aspects of plant biology are highly conserved across the Triticeae species but so also were many mutant loci. Received: 19 June 2000 / Accepted: 18 October 2000     

Establishment of introgression libraries in hybrid rye (Secale cereale L.) from an Iranian primitive accession as a new tool for rye breeding and genomics

Genetic diversity of elite breeding material can be increased by introgression of exotic germplasm to ensure long-term selection response. The objective of our study was to develop and characterize the first two rye introgression libraries generated by marker-assisted backcrossing and demonstrate their potential application for improving the baking quality of rye. Starting from a cross between inbred line L2053-N (recurrent parent) and a heterozygous Iranian primitive population Altevogt 14160 (donor) two backcross (BC) and three selfing generations were performed to establish introgression libraries A and B. Amplified fragment length polymorphisms (AFLP markers) and simple sequences repeats (SSRs) were employed to select and characterize candidate introgression lines (pre-ILs) from BC(1) to BC2S3. The two introgression libraries comprise each 40 BC2S3 pre-ILs. For analyzing the phenotypic effects of the exotic donor chromosome segment (DCS) we evaluated the per se performance for pentosan and starch content in replicated field trials at each of four locations in 2005 and 2006. Introgression library A and B cover 74 and 59% of the total donor genome, respectively. The pre-ILs contained mostly two to four homozygous DCS, with a mean length of 12.9 cM (A) and 10.0 cM (B). We detected eight (A) and nine (B) pre-ILs with a significant (P<0.05) higher pentosan content and two pre-ILs (B) with a significant (P<0.05) higher starch content than the elite recurrent parent. Thus, our results indicate that exotic genetic resources in rye carry favorable alleles for baking quality traits, which can be exploited for improving the elite breeding material by marker-assisted selection (MAS). These introgression libraries can substantially foster rye breeding programs and provide a promising opportunity to proceed towards functional genomics.     

Fluctuations in numbers in box populations of Drosophila and selective genetic mechanism of their regulation

Box populations of Drosophila melanogaster are characterized by two types of periodical fluctuations of numbers: with low and high frequency. High frequency fluctuations are determined by existence of preimago and imago stages and subsequent delay in density-dependent limitation of imago reproduction, duration of which is determined by time of preimago stage. The period of these fluctuations should be limited within two generation, that is confirmed by experimental data. Low frequency fluctuations with the period of 13-15 generations are the result of ecological density-dependent effect. In this case during pick density one can observe continuous degradation of population (i.e. decrease in fecundity and life time of imago) and following decrease in numbers. Temporary changes in fecundity of females and their offspring of the second generation are positively correlated with low frequency fluctuations in numbers. Such relationships show the possibility of density-dependent, cyclic, genetic changes in fecundity connected with fluctuations in numbers. It means that at the phase of growth in numbers when the density is still low, the selection is directed to the individuals with high fecundity sensible to overpopulation. The phase of decline in numbers is connected with high density and selection directed to the individuals with low fecundity in low density populations. The changes in genetic structure of fluctuating population lead to the weakening of this fluctuations and to the maintaining of population under such conditions.     

Dispersal of the flea Ctenophyllus hirticrus and spreading of plague epizooties in Gorny Altai

Gradual dispersion of an abundant flea species Ctenophyllus hirticrus specific to the Pallas's pika (the main plague carrier), is revealed in the Gorno-Altai natural plague focus on the territory, occupied by two populations of this lagomorph. Spreading of Yersinia pestis in these areas took place a short time later the rise of this ectoparasite's abundance. It is supposed that the colonization of these areas by C. hirticrus was one of the factors determined epizooties spreading within the focus and formation of new sites of stable Y. pestis preservation.     

Comparative mapping of a gibberellic acid-insensitive dwarfing gene (Dwf2) on chromosome 4HS in barley

 We report the genetic mapping of Dwf2, a dominant gibberellic acid (GA₃)-insensitive dwarfing gene which has been previously described to cause a very short growth habit in barley (Hordeum vulgare) mutant ‘93/B694’. Using RFLP and microsatellite markers we performed segregation analysis in an F₂ population comprising 86 individuals developed from a cross of ‘93/B694’ (Dwf2) with ‘Bonus M2’ (dwf2). Dwf2 was mapped on the short arm of barley chromosome 4H proximal to microsatellite marker XhvOle (5.7 cM) and distal to RFLP marker Xmwg2299 (18.3 cM). The genetic localization of the Dwf2 gene at a homoeologous position to the multiallelic Rht-B1 and Rht-D1 loci in wheat suggests synteny of GA-insensitive dwarfing genes within the Triticeae. Moreover, the extremely prostrate growth habit exhibited in barley ‘93/B694’ (Dwf2) resembles that of wheat plants carrying the genes Rht-B1c (Rht3) or Rht-D1c (Rht10). Received: 1 July 1998 / Accepted: 17 September 1998