Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

Cao, Dong; Wang, Dongxia; Li, Shiming; Li, Yun; Hao, Ming; Liu, Baolong

doi:10.1007/s00122-022-04064-5

Cited by 6 publications

(7 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…GBS coverage analysis represents a convenient and fast method for analyzing the genome composition of allopolyploids 32 , 33 . We found that the presence of parental incompatible alleles triggers major rearrangements in wheat and rye chromosomes in wheat-rye hybrids.…”

Section: Discussionmentioning

confidence: 99%

“…The loss of rye chromosomes was compensated by an extra pair of 2D or A-genome chromosomes (possibly 2A) in plants with 2n = 56. The authors suggested that the loss of 2R and 5RS with their replacement by chromosomes of the D and A genome contributes to the improvement of octoploid triticale 33 , 53 . The vast changes in spike architecture caused by nullisomy of the 2R and 5R chromosomes of rye were found in androgenic offspring of hexaploid triticale (× Triticosecale Wittmack).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Major chromosome rearrangements in intergeneric wheat × rye hybrids in compatible and incompatible crosses detected by GBS read coverage analysis

Tikhenko,

Haupt,

Fuchs

et al. 2024

Sci Rep

View full text Add to dashboard Cite

The presence of incompatibility alleles in primary amphidiploids constitutes a reproductive barrier in newly synthesized wheat-rye hybrids. To overcome this barrier, the genome stabilization process includes large-scale chromosome rearrangements. In incompatible crosses resulting in fertile amphidiploids, the elimination of one of the incompatible alleles Eml-A1 or Eml-R1b can occur already in the somatic tissue of the wheat × rye hybrid embryo. We observed that the interaction of incompatible loci Eml-A1 of wheat and Eml-R1b of rye after overcoming embryo lethality leads to hybrid sterility in primary triticale. During subsequent seed reproductions (R1, R2 or R3) most of the chromosomes of A, B, D and R subgenomes undergo rearrangement or eliminations to increase the fertility of the amphidiploid by natural selection. Genotyping-by-sequencing (GBS) coverage analysis showed that improved fertility is associated with the elimination of entire and partial chromosomes carrying factors that either cause the disruption of plant development in hybrid plants or lead to the restoration of the euploid number of chromosomes (2n = 56) in the absence of one of the incompatible alleles. Highly fertile offspring obtained in compatible and incompatible crosses can be successfully adapted for the production of triticale pre-breeding stocks.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Major chromosome rearrangements in intergeneric wheat × rye hybrids in compatible and incompatible crosses detected by GBS read coverage analysis

Tikhenko,

Haupt,

Fuchs

et al. 2024

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Due to the lack of a high-quality triticale reference genome, wheat and rye reference genomes are useful resources for the identification of candidate genes that underlie markers associated with IVD traits in triticale [ 8 ]. Based on MTAs, candidate genes were identified which were of particular relevance for variation in IVD because they are putatively involved in plasma membrane transport, cytoskeleton organisation, enzyme activity, carbohydrate metabolic processes, protein phosphorylation, and sterol biogenesis (Table 3 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study for in vitro digestibility and related traits in triticale forage

De Zutter,

Piro,

Maenhout

et al. 2024

BMC Plant Biol

View full text Add to dashboard Cite

Background Triticale is making its way on dairy farms as an alternative forage crop. This requires the availability of high-yielding triticale varieties with good digestibility. Triticale forage breeding mainly focussed on biomass yield, but efforts to improve digestibility are increasing. We previously investigated the interrelationships among different quality traits in soft dough triticale: starch, acid detergent fibre and in vitro digestibility of organic matter (IVOMD) and of neutral detergent fibre (IVNDFD) of the total plant, IVNDFD and Klason lignin of the stems, and ear proportion and stem length. Here we determine the genetic control of these traits, using a genome-wide association (GWAS) approach. A total of 33,231 DArTseq SNP markers assessed in a collection of 118 winter triticale genotypes, including 101 varieties and 17 breeding lines, were used. Results The GWAS identified a total of 53 significant marker-trait associations (MTAs). The highest number of significantly associated SNP markers (n = 10) was identified for total plant IVNDFD. A SNP marker on chromosome 1A (4211801_19_C/T; 474,437,796 bp) was found to be significantly associated with ear proportion, and plant and stem IVNDFD, with the largest phenotypic variation for ear proportion (R²p = 0.23). Based on MTAs, candidate genes were identified which were of particular relevance for variation in in vitro digestibility (IVD) because they are putatively involved in plasma membrane transport, cytoskeleton organisation, carbohydrate metabolic processes, protein phosphorylation, and sterol and cell wall biogenesis. Interestingly, a xyloglucan-related candidate gene on chromosome 2R, SECCE2Rv1G0126340, was located in close proximity of a SNP significantly associated with stem IVNDFD. Furthermore, quantitative trait loci previously reported in wheat co-localized with significantly associated SNP markers in triticale. Conclusions A collection of 118 winter triticale genotypes combined with DArTseq SNP markers served as a source for identifying 53 MTAs and several candidate genes for forage IVD and related traits through a GWAS approach. Taken together, the results of this study demonstrate that the genetic diversity available in this collection can be further exploited for research and breeding purposes to improve the IVD of triticale forage.

show abstract

“…Hexaploid triticale contains wheat and rye genomes, and shows relatively superior vigor and reproductive stability ( Lukaszewski and Gustafson, 1987 ; Cheng and Murata, 2002 ). Studies on genome-wide diversity have revealed diversified genetic structures in rye and Triticale germplasm ( Bolibok-Bragoszewska et al., 2014 ; Sun et al., 2022 ; Cao et al., 2022 ). Among the rye chromosomes, the S. cereale chromosome 6R has displayed rapid structural change and high levels of heterogeneity of heterochromatin blocks, which has been revealed by FISH using tandem repeat probes on different rye cultivars ( Guo et al., 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Molecular and cytogenetic dissection of stripe rust resistance gene Yr83 from rye 6R and generation of resistant germplasm in wheat breeding

Zhang

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Rye 6R-derived stripe rust resistance gene Yr83 in wheat background was physically mapped to fraction length (FL) 0.87-1.00 on the long arm by non-denaturing-fluorescence in situ hybridization (ND-FISH), Oligo-FISH painting and 6R-specific PCR markers.Stripe rust resistance gene Yr83 derived from chromosome 6R of rye (Secale cereale) “Merced” has displayed high resistance to both Australian and Chinese wheat stripe rust isolates. With the aim to physically map Yr83 to a more precise region, new wheat- 6R deletion and translocation lines were produced from derived progenies of the 6R(6D) substitution line. The non-denaturing fluorescence in situ hybridization (ND-FISH) patterns of 6R were established to precisely characterize the variations of 6R in different wheat backgrounds. Comparative ND-FISH analysis localized the breakpoints of 6RL chromosomes relative to Oligo-pSc200 and Oligo-pSc119.2 rich sites in deletion lines. Molecular marker and resistance analyses confirmed that Yr83 is physically located at the fraction length (FL) 0.87-1.00 of 6RL and covers the corresponding region of 806-881 Mb in the reference genome of Lo7. Oligo-FISH painting demonstrated that the region carrying Yr83 is syntenic to the distal end of long arm of homoeologous group 7 of the Triticeae genome. The developed wheat-6R lines carrying the Yr83 gene will be useful for breeding for rust resistance.

show abstract

Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

Abstract: Key message The genetic diversity and loci underlying agronomic traits were analysed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.

Cited by 6 publications

References 70 publications

Major chromosome rearrangements in intergeneric wheat × rye hybrids in compatible and incompatible crosses detected by GBS read coverage analysis

Major chromosome rearrangements in intergeneric wheat × rye hybrids in compatible and incompatible crosses detected by GBS read coverage analysis

Genome-wide association study for in vitro digestibility and related traits in triticale forage

Molecular and cytogenetic dissection of stripe rust resistance gene Yr83 from rye 6R and generation of resistant germplasm in wheat breeding

Contact Info

Product

Resources

About