Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia

Abstract

The genetic control of plant architecture is a promising approach to breed desirable cultivars, particularly in ornamental flowers. In this study, the F1 population (142 seedlings) derived from Lagerstroemia fauriei (non-dwarf) × L. indica ‘Pocomoke’ (dwarf) was phenotyped for six traits (plant height (PH), internode length (IL), internode number, primary lateral branch height (PLBH), secondary lateral branch height and primary branch number), and the IL and PLBH traits were positively correlated with the PH trait and considered representative indexes of PH. Fifty non-dwarf and dwarf seedlings were pooled and subjected to a specific-locus amplified fragment sequencing (SLAF-seq) method, which screened 1221 polymorphic markers. A total of 3 markers segregating between bulks were validated in the F1 population, with the M16337 and M38412 markers highly correlated with the IL trait and the M25207 marker highly correlated with the PLBH trait. These markers provide a predictability of approximately 80% using a single marker (M25207) and a predictability of 90% using marker combinations (M16337 + M25207) in the F1 population, which revealed that the IL and the PLBH traits, especially the PLBH, were the decisive elements for PH in terms of molecular regulation. Further validation was performed in the BC1 population and a set of 28 Lagerstroemia stocks using allele-specific PCR (AS-PCR) technology, and the results showed the stability and reliability of the SNP markers and the co-determination of PH by multiple genes. Our findings provide an important theoretical and practical basis for the early prediction and indirect selection of PH using the IL and the PLBH, and the detected SNPs may be useful for marker-assisted selection (MAS) in crape myrtle.

Transcriptome profiles reveal that gibberellin-related genes regulate weeping traits in crape myrtle

“…Research on the plant architecture of crape myrtle is mainly focused on dwarf traits. Two markers that are highly correlated with internode length and one marker that is highly correlated with primary lateral branch height have been validated in crape myrtle 34 . The analysis of transcriptome and hormone levels in dwarf and non-dwarf crape myrtles suggested that internode length is controlled by an interaction between auxin and GA4 32 .…”

Untitled

“…To test the amplification efficiency of the selected EST-SSRs, the F1 segregating population was employed in this study (Ye et al, 2016). Seven Lagerstroemia species were used to confirm the cross-species transferability of selected EST-SSR markers, including L. indica, L. fauriei, L. speciosa, L. excelsa, L. caudata, L. limii and L. subcostata.…”

“…And then a set of 30 primer pairs were selected according to their polymorphism and identification ability, in order to analyze the genetic diversity among 73 accessions, and transferability across seven Lagerstroemia species. The PCR amplification conditions and procedures were referenced from Ye et al (2016). For analysis of genetic relationship, the forward primers of SSRs were elongated from M13 universal sequences appended to the 5'-end (Schuelke, 2000).…”

“…He et al (2012) genotyped all the 96 Lagerstroemia samples and devided them into three distinct groups based on genetic distance. Thus, it provides a shortcut to perform the genetic studies and improvement of these valuable traits in crape myrtle by molecular markers (Ye et al, 2016).…”

Untitled

“…In our previous studies, the F1 population was used to investigate the genetic inheritance of plant architecture traits (Ye et al, 2015(Ye et al, , 2016. Herein, we performed the transcriptome analysis for the parents in order to screen the target genes, as well as the massive EST-SSR markers.…”