Development and Chromosome Mapping of 81 New Wheat EST-SSR Markers and Application for Characterizing Rye Chromosomes Added in Wheat: Development and Chromosome Mapping of 81 New Wheat EST-SSR Markers and Application for Characterizing Rye Chromosomes Added in Wheat

A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments

Background

Common wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat varieties that maintain yield (YD) under moderate or even intense nitrogen (N) deficiency can adapt to low input management systems. A detailed genetic map is necessary for both wheat molecular breeding and genomics research. In this study, an F_6:7 recombinant inbred line population comprising 188 lines was used to construct a novel genetic map and subsequently to detect quantitative trait loci (QTL) for YD and response to N stress.

Results

A genetic map consisting of 591 loci distributed across 21 wheat chromosomes was constructed. The map spanned 3930.7 cM, with one marker per 6.7 cM on average. Genomic simple sequence repeat (g-SSR), expressed sequence tag-derived microsatellite (e-SSR), diversity arrays technology (DArT), sequence-tagged sites (STS), sequence-related amplified polymorphism (SRAP), and inter-simple sequence repeat (ISSR) molecular markers were included in the map. The linear relationships between loci found in the present map and in previously compiled physical maps were presented, which were generally in accordance. Information on the genetic and physical positions and allele sizes (when possible) of 17 DArT, 50 e-SSR, 44 SRAP, five ISSR, and two morphological markers is reported here for the first time. Seven segregation distortion regions (SDR) were identified on chromosomes 1B, 3BL, 4AL, 6AS, 6AL, 6BL, and 7B. A total of 22 and 12 QTLs for YD and yield difference between the value (YDDV) under HN and the value under LN were identified, respectively. Of these, QYd-4B-2 and QYddv-4B, two major stable QTL, shared support interval with alleles from KN9204 increasing YD in LN and decreasing YDDV. We probe into the use of these QTLs in wheat breeding programs. Moreover, factors affecting the SDR and total map length are discussed in depth.

Conclusions

This novel map may facilitate the use of novel markers in wheat molecular breeding programs and genomics research. Moreover, QTLs for YD and YDDV provide useful markers for wheat molecular breeding programs designed to increase yield potential under N stress.

Development and application of EST-based markers specific for chromosome arms of rye (Secale cereale L.)

To develop a set of molecular markers specific for the chromosome arms of rye, a total of 1,098 and 93 primer pairs derived from the expressed sequence tag (EST) sequences distributed on all 21 wheat chromosomes and 7 rye chromosomes, respectively, were initially screened on common wheat 'Chinese Spring' and rye cultivar 'Imperial'. Four hundred and fourteen EST-based markers were specific for the rye genome. Seven disomic chromosome addition lines, 10 telosomic addition lines and 1 translocation line of 'Chinese Spring-Imperial' were confirmed by genomic in situ hybridization and fluorescencein situ hybridization, and used to screen the rye-specific markers. Thirty-one of the 414 markers produced stable specific amplicons in 'Imperial', as well as individual addition lines and were assigned to 13 chromosome arms of rye except for 6RS. Six rye cultivars, wheat cultivar 'Xiaoyan 6' and accessions of 4 wheat relatives were then used to test the specificity of the 31 EST-based markers. To confirm the specificity, 4 wheat-rye derivatives of 'Xiaoyan 6 × German White', with chromosomes 1RS, 2R and 4R, were amplified by some of the EST-based markers. The results indicated that they can effectively be used to detect corresponding rye chromosomes or chromosome arms introgressed into a wheat background, and hence to accelerate the utilization of rye genes in wheat breeding.