Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

BACKGROUND

Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.

RESULTS

We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264-364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.

CONCLUSIONS

As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.

QTL mapping and transcriptome analysis identify candidate genes regulating pericarp thickness in sweet corn

BACKGROUND

In recent years, the planting area of sweet corn in China has expanded rapidly. Some new varieties with high yields and good adaptabilities have emerged. However, the improvement of edible quality traits, especially through the development of varieties with thin pericarp thickness, has not been achieved to date. Pericarp thickness is a complex trait that is the key factor determining the edible quality of sweet corn. Genetic mapping combined with transcriptome analysis was used to identify candidate genes controlling pericarp thickness.

RESULTS

To identify novel quantitative trait loci (QTLs) for pericarp thickness, a sweet corn BC₄F₃ population of 148 lines was developed using the two sweet corn lines M03 (recurrent parent) and M08 (donor parent). Additionally, a high-density genetic linkage map containing 3876 specific length amplified fragment (SLAF) tags was constructed and used for mapping QTLs for pericarp thickness. Interestingly, 14 QTLs for pericarp thickness were detected, and one stable QTL (qPT10-5) was detected across multiple years, which explained 7.78-35.38% of the phenotypic variation located on chromosome 10 (144,631,242-145,532,401). Forty-two candidate genes were found within the target region of qPT10-5. Moreover, of these 42 genes, five genes (GRMZM2G143402, GRMZM2G143389, GRMZM2G143352, GRMZM6G287947, and AC234202.1_FG004) were differentially expressed between the two parents, as revealed by transcriptome analysis. According to the gene annotation information, three genes might be considered candidates for pericarp thickness. GRMZM2G143352 and GRMZM2G143402 have been annotated as AUX/IAA transcription factor and ZIM transcription factor, respectively, while GRMZM2G143389 has been annotated as FATTY ACID EXPORT 2, chloroplastic.

CONCLUSIONS

This study identified a major QTL and candidate genes that could accelerate breeding for the thin pericarp thickness variety of sweet corn, and these results established the basis for map-based cloning and further functional research.