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.
Introgression libraries can be used to localize genomic regions carrying quantitative trait loci (QTL). We used this approach to detect QTL regions affecting the per se performance of agronomic and quality traits with two rye (Secale cereale L.) introgression libraries. Our objectives were to detect candidate introgression lines (pre-ILs) that have a different per se performance than the recurrent parent and to identify the underlying QTL regions. The introgression libraries containing 40 BC 2 S 3 lines each were established with marker-assisted backcrossing from crosses of the heterozygous Iranian primitive rye accession Altevogt 14160 and the elite inbred line L2053-N. To assess the phenotypic effect of the donor chromosome segments (DCS) the pre-ILs were evaluated for grain yield, plant height, thousand-kernel weight, test weight, falling number and protein content in replicated field trials at five locations in Germany over 2 years. In total, 58 significant (P < 0.05) differences between pre-ILs and L2053-N were observed in each introgression library. The DCS in pre-ILs differing from the recurrent parent possess most likely the responsible QTL. Genomic regions carrying favourable QTL alleles were detected for test weight, thousand-kernel weight and protein content. We conclude that Altevogt 14160 can not only be used to enrich the genetic variation of the restricted hybrid rye gene pools but will also allow the breeder to efficiently detect favourable QTL for marker-assisted selection.
The performance of hybrids can be predicted with gene expression data from their parental inbred lines. Implementing such prediction approaches in breeding programs promises to increase the efficiency of hybrid breeding. The objectives of our study were to compare the accuracy of prediction models employing multiple linear regression (MLR), partial least squares regression (PLS), support vector machine regression (SVM), and transcriptome-based distances (D(B)). For a factorial of 7 flint and 14 dent maize lines, the grain yield of the hybrids was assessed and the gene expression of the parental lines was profiled with a 56k microarray. The accuracy of the prediction models was measured by the correlation between predicted and observed yield employing two cross-validation schemes. The first modeled the prediction of hybrids when testcross data are available for both parental lines (type 2 hybrids), and the second modeled the prediction of hybrids when no testcross data for the parental lines were available (type 0 hybrids). MLR, SVM, and PLS resulted in a high correlation between predicted and observed yield for type 2 hybrids, whereas for type 0 hybrids D(B) had greater prediction accuracy. The regression methods were robust to the choice of the set of profiled genes and required only a few hundred genes. In contrast, for an accurate hybrid prediction with D(B), 1,000-1,500 genes were required, and the prediction accuracy depended strongly on the set of profiled genes. We conclude that for prediction within one set of genetic material MLR is a promising approach, and for transferring prediction models from one set of genetic material to a related one, the transcriptome-based distance D(B) is most promising.
Introgression libraries facilitate the identification of favorable exotic alleles or genomic regions, which can be exploited for improving elite breeding material. We evaluated the first two introgression libraries in rye (Secale cereale L.) on the phenotypic and molecular level. Our objectives were to detect candidate introgression lines (pre-ILs) with a better testcross performance than the recurrent parent and identify donor chromosome segments (DCS) responsible for the improved performance. We introduced DCS from the self-incompatible heterozygous exotic Iranian primitive rye accession Altevogt 14160 (donor) into the genetic background of the elite inbred line L2053-N (recurrent parent) by marker-assisted backcrossing and developed 40 BC(2)S(3) lines in each introgression library. Testcross performance for three agronomic and six quality traits was evaluated in replicated field trials across two testers at five locations over 2 years. The phenotypic effect of the DCS was analyzed for all traits. The pre-ILs had on average a testcross performance comparable to that of the recurrent parent. Significant (P < 0.05) differences between individual pre-ILs and the recurrent parent were detected for all traits except for heading date. For more than 60% of the significant (P < 0.05) differences, the pre-ILs were superior to the recurrent parent. For some pre-ILs, specific DCS were identified containing presumably quantitative trait loci responsible for the superior hybrid performance. Consequently, our study revealed that the development and employment of introgression libraries offers the opportunity for a targeted increase of genetic diversity of elite rye material for hybrid performance of agronomically important traits.
Plant height is an important trait for breeding and as fitness criterion in natural populations of rye (Secale cereale L.). Our objectives were to investigate the inheritance of plant height in rye introgression libraries and estimate the covariation between per se and testcross performance. Two introgression libraries containing each of 40 BC 2 S 3 candidate introgression lines (pre-ILs) were tested at five locations in two years for per se and testcross performance. Donor population was the Iranian primitive rye accession Altevogt 14160. Plant height of the donor population was 145 ± 3.6 cm as population and 152 ± 2.9 and 132 ± 2.8 cm when crossed to the two testers, respectively. Pre-ILs were much closer to the recurrent parent, but still most of them exceeded the recurrent parent in per se performance. Estimates of the genotypic variance were significant (P = 0.01) for both per se and testcross performance. Entry-mean heritabilities were high in both libraries (0.97 and 0.94, respectively). Donor chromosome segments (DCS) of 59 of 72 pre-ILs had a significant (P = 0.05) effect on plant height compared to the recurrent parent. For the testcrosses, 10 preILs still contributed DCS with significantly (P = 0.05) taller effects. Genotypic correlations between pre-ILs per se and as testcrosses were moderate for the two testers. In conclusion, plant height per se has a complex inheritance with many loci spread across the entire genome. Hybrid breeding, however, facilitates the use of genetic resources because the tallness is less pronounced in the testcrosses. Plant height is a major adaptive trait affecting fitness in natural plant populations and is an important selection criterion in breeding programmes. Winter rye (Secale cereale L.) is the tallest of all small grain cereals. Its primary centre of origin is not known precisely, but it appears to be south-western Asia, essentially the same area of origin as common wheat (Triticum aestivum L.), barley (Hordeum vulgare L.) and oat (Avena sativa L.; Sencer and Hawkes 1980). Wild populations of rye invaded wheat and barley fields during the early days of cultivation and gave rise to weedy ryes with varying degrees of rachis brittleness. Cultivated rye was selected from these weedy ryes for non-brittle rachis and bigger caryopsis unconsciously as well as consciously by man. A number of weedy rye types are still found in grain fields and along ditchbanks and roadsides throughout the Middle East countries (Stutz 1972). Such primitive rye collected in Iran often exceeds 1.6-1.8 m in height.In practical rye breeding, shorter varieties are favoured because of reduced risk of lodging and easier handling during harvest. Two dominant and nine recessive reducing height (rht) or dwarfing (dw) genes have been described in rye (Bo¨rner et al. 1996). However, in sharp contrast to wheat, these genes play no role in practical growing because of their yield penalty and reduced yield stability. As rye is often grown on light, shallow sandy soils suffering from reduced water and nutrien...
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