Abstract
Main conclusion
This genetic map for Agropyron Gaertn. contained 1023 markers on seven linkage groups, with a total of 907.8 cM and an average distance of 1.5 cM between adjacent loci.
Many wheat- Agropyron cristatum derivative lines exhibit superior agronomic traits, and part of them are valuable for future wheat breeding. To date, no high-density genetic map for Agropyron Gaertn. has been published. Specific-locus amplified fragment sequencing (SLAF-seq), a recently developed strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms (SNPs), was employed in this study to develop sufficient markers for a segregating Agropyron F1 population derived from an interspecific cross between two cross-pollinated diploid collections A. cristatum (L.) Beauv. ‘Z1842’ and A. mongolicum Keng ‘Z2098’. In total, we obtained raw data consisting of 128,932,358 pair-end reads of ~80 bp long after sequencing. Then 69,325 high-quality SLAFs were detected, of which 26,248 SLAFs were polymorphic and 1752 of the polymorphic markers were used for the genetic map construction. The final map contained 1023 markers on the seven linkage groups (LGs), which spanned a total of 907.8 cM with an average number of 146 markers and 89 loci per LG and an average distance of 1.5 cM between adjacent loci. To our knowledge, this map is the densest genetic linkage map for Agropyron so far. Through BLAT alignment of Agropyron SLAF marker sequences with the draft genome assemblies of wheat and barley, the Agropyron LGs were assigned as LG1-7 according to their corresponding homoeologous chromosomal groups of wheat. Results of this study will not only provide a platform for gene/QTL fine mapping, but also serve as a reference to assist the assembling of the P genome sequence in future.
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Abbreviations
- Agropyron :
-
Agropyron Gaertn.
- CP:
-
Cross-pollinated
- LG:
-
Linkage group
- SLAF-seq:
-
Specific-locus amplified fragment sequencing
- SNP:
-
Single nucleotide polymorphism
References
Chen D, Zhang J, Wang J, Yang X, Liu W, Gao A, Li X, Li L (2012) Inheritance and availability of high grain number per spike in two wheat germplasm lines. J Integr Agr 11:1409–1416
Chen S, Ma X, Zhang X, Huang L, Zhou J (2013) Genetic diversity and relationships among accessions of five crested wheatgrass species (Poaceae: Agropyron) based on gliadin analysis. Genet Mol Res 12:5704
Dewey DR (1984) The genomic system of classification as a guide to intergeneric hybridization with the perennial Triticeae. In: Gustafson JP (ed) Gene manipulation in plant improvement, 16th Stadler Genetics Symposium. Springer, US, New York, pp 209–279
Dong Y, Zhou R, Xu S, Li L, Cauderon Y, Wang R (1992) Desirable characteristics in perennial Triticeae collected in China for wheat improvement. Hereditas 116:175–178
Ford-Lloyd BV, Schmidt M, Armstrong SJ, Barazani O, Engels J, Hadas R, Hammer K, Kell SP, Kang D, Khoshbakht K (2011) Crop wild relatives—undervalued, underutilized and under threat? Bioscience 61:559–565
Han H, Bai L, Su J, Zhang J, Song L, Gao A, Yang X, Li X, Liu W, Li L (2014) Genetic rearrangements of six wheat–Agropyron cristatum 6P addition lines revealed by molecular markers. PLoS ONE 9:e91066
Hu C-Y, Lee T-C, Tsai H-T, Tsai Y-Z, Lin S-F (2013) Construction of an integrated genetic map based on maternal and paternal lineages of tea (Camellia sinensis). Euphytica 191:141–152
Hyten D, Cannon S, Song Q, Weeks N, Fickus E, Shoemaker R, Specht J, Farmer A, May G, Cregan P (2010) Highthroughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genom 11:38
Kent WJ (2002) BLAT—the BLAST-like alignment tool. Genome Res 12:656–664
Li L, Yang X, Li X, Dong Y, Chen X (1998) Introduction of desirable genes from Agropyron cristatum into common wheat by intergeneric hybridization. Sci Agric Sinica 31:1–6
Liu W, Luan Y, Wang J, Wang X, Su J, Zhang J, Yang X, Gao A, Li L (2010) Production and identification of wheat- Agropyron cristatum (1.4P) alien translocation lines. Genome 53:472–481
Liu D, Ma C, Hong W, Huang L, Liu M, Liu H, Zeng H, Deng D, Xin H, Song J (2014) Construction and analysis of high-density linkage map using high-throughput sequencing data. PLoS ONE 9:e98855
Luan Y, Wang X, Liu W, Li C, Zhang J, Gao A, Wang Y, Yang X, Li L (2010) Production and identification of wheat- Agropyron cristatum 6P translocation lines. Planta 232:501–510
Ochoa V, Madrid E, Said M, Rubiales D, Cabrera A (2015) Molecular and cytogenetic characterization of a common wheat- Agropyron cristatum chromosome translocation conferring resistance to leaf rust. Euphytica 201:89–95
Pfender W, Saha M, Johnson E, Slabaugh M (2011) Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor Appl Genet 122:1467–1480
Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15:8–15
Qi Z, Huang L, Zhu R, Xin D, Liu C, Han X, Jiang H, Hong W, Hu G, Zheng H (2014) A high-density genetic map for soybean based on specific length amplified fragment sequencing. PLoS ONE 9:e104871
Song L, Jiang L, Han H, Gao A, Yang X, Li L, Liu W (2013) Efficient induction of wheat- Agropyron cristatum 6P translocation lines and GISH detection. PLoS ONE 8:e69501
Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: Join Map. Plant J 3:739–744
Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H (2013) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE 8:e58700
Wang N, Fang L, Xin H, Wang L, Li S (2012) Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC Plant Biol 12:148
Wu J, Yang X, Wang H, Li H, Li L, Li X, Liu W (2006) The introgression of chromosome 6P specifying for increased numbers of florets and kernels from Agropyron cristatum into wheat. Theor Appl Genet 114:13–20
Wu M, Zhang J, Wang J, Yang X, Gao A, Zhang X, Liu W, Li L (2010) Cloning and characterization of repetitive sequences and development of SCAR markers specific for the P genome of Agropyron cristatum. Euphytica 172:363–372
Yu X, Li X, Ma Y, Yu Z, Li Z, Gulick P (2012) A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers. Genome 55:327–335
Zhang Y, Wang L, Xin H, Li D, Ma C, Ding X, Hong W, Zhang X (2013) Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Plant Biol 13:141
Zhang J, Liu W, Han H, Song L, Bai L, Gao Z, Zhang Y, Yang X, Li X, Gao A, Li L (2015) De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat. Genomics. doi:10.1016/j.ygeno.2015.04.003
Acknowledgments
This work was supported by the grants from the National Basic Research Program of China (973 Grant No. 2011CB100104), the National Natural Science Foundation of China (Grant No. 31471493), and the National High Technology Research and Development Program of China (863 Grant No. 2011AA100101).
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Y. Zhang, J. Zhang and L. Huang contributed equally to this work.
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425_2015_2372_MOESM1_ESM.tif
Supplementary material 1 (TIFF 952 kb). Fig. S1 Examples for the five segregation types for population type CP. * indicates SNP. P, paternal parent; M, maternal parent. aa, ab and ac are tags for three individuals. The number under P, M, aa, ab and ac indicates sequencing depth. “XXXXXXXXXX” represents middle unknown fragment in a marker sequence, and the base number is also unknown. According to JoinMap 4 manual, < ab × ad > , locus heterozygous in both parents, four alleles; < ef × eg > , locus heterozygous in both parents, three alleles; < hk × hk > , locus heterozygous in both parents, two alleles; < lm × ll > , locus heterozygous in the first parents, two alleles; < nn × np > , locus heterozygous in the second parents, two alleles
425_2015_2372_MOESM11_ESM.xlsx
Supplementary material 11 (XLSX 786 kb). Table S4 Genotype data of 1752 SLAF markers in the F1 individuals for the map construction
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Supplementary material 13 (XLSX 39 kb). Table S6 Genotype frequencies of segregation distortion SLAF markers in the F1 individuals
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Supplementary material 14 (XLSX 81 kb). Table S7 Partial sequences of contigs of wheat and barley showing ≥ 80 % sequence identity with Agropyron marker sequences
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Supplementary material 15 (XLSX 24 kb). Table S8 Genetic positions of Agropyron markers and their homologous contigs in wheat and barley. The contigs, which were homologous with Agropyron markers and had no information about chromosomal localization and genetic position, were also listed
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Zhang, Y., Zhang, J., Huang, L. et al. A high-density genetic map for P genome of Agropyron Gaertn. based on specific-locus amplified fragment sequencing (SLAF-seq). Planta 242, 1335–1347 (2015). https://doi.org/10.1007/s00425-015-2372-7
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DOI: https://doi.org/10.1007/s00425-015-2372-7