Association of single nucleotide polymorphisms in LpIRI1 gene with freezing tolerance traits in perennial ryegrass

Abstract

Perennial ryegrass is an important agricultural crop, however, it is susceptible to winterkill. Freezing injury is caused primarily by ice formation. The LpIRI1 protein has the potential to inhibit ice recrystallization, thus minimize the damage. An association study was conducted using single nucleotide polymorphisms obtained through allele sequencing of the LpIRI1 gene and phenotypic data were collected using two phenotyping platforms in a perennial ryegrass association mapping population of 76 diverse genotypes. Winter survival (FWS) was evaluated under field conditions, while tiller survival (PTS) and electrolyte leakage (EL) at -8 and -12°C were determined under controlled-environment conditions. Proline content (PC) in cold-acclimated plants was measured prior to the freezing test. Significant variation in FWS, PTS, EL and PC was observed among genotypes in our panel. EL and PTS revealed significant negative correlations at -8°C (r s = -0.40) and -12°C (r s = -0.49). PC, however, did not show significant correlations with any of the measured traits, while FWS was correlated (r s = -0.48) with EL at -12°C. The LpIRI1 gene was found to be highly polymorphic with an average SNP frequency of 1 SNP per 16 bp. Association analysis revealed two non-synonymous SNPs being associated with increased EL, both located in the LpIRI1 leucinerich repeat. The results indicate that allelic variation in the LpIRI1 gene plays an important role in the cell membrane integrity of perennial ryegrass during freezing, and can be exploited for developing more freezing tolerant cultivars.

Perennial Ryegrass Yield Performance under Abiotic Stress

“…The winters of 2015 and 2016 were characterized by short (2-6 wk) periods of lower than -10°C temperatures in January in Lithuania. Numerous studies focus on genetic factors behind perennial ryegrass freezing tolerance as a key component in successful overwintering (Aleliūnas et al, 2015;Yu et al, 2015;Paina et al, 2016), yet most of them were conducted using only diploid genotypes, whereas the data on differences in resistance between diploid and tetraploid plants have been relatively scarce. Tetraploid populations tended to be slightly more resistant to winterkill, yet the differences were not statistically significant.…”

LpBRI1 polymorphism association with flag leaf architecture in perennial ryegrass

“…SNPs with minor allele frequency of less than 5% were excluded from further analysis. Population structure and relative kinship estimations were based on AFLP markers as described in Aleliūnas et al (2015). Specific primers, flanking 3bp INDEL polymorphism in LpBRI1 gene, were used to identify allelic variation for this INDEL in broader perennial ryegrass population, consisting of 213 genotypes.…”

“…In this study, flag leaf was associated with INDEL in 3'UTR region of LpBRI1 gene, located on LG 3 in perennial ryegrass. The gene codes for cell surface receptor kinase brassinosteroid-insensitive 1 (BRI1) (reviewed in Fariduddin et al, 2014) and brassinosteroids (BR), plant-originated steroidal lactones, are well known for promoting growth (Choe, 2006), increasing the leaf number and area (Bhat et al, 2011) as well as having a favourable effect on the yield of plants (Janeczko et al, 2010). The INDEL polymorphism identified in this study cannot alter the activity of the protein through change in amino acid composition as it is allocated in non-coding region.…”

Identification of an ice recrystallisation inhibition gene family in winter‐hardy wheat and its evolutionary relationship to other members of the Triticeae

“…The initial electrical conductivity (S 1 ) was measured using a DDS‐IIA detector (Shanghai, China), and then the final electrical conductivity (S 2 ) was measured after boiling for 10 min. Relative electrolyte leakage (L) was calculated as: (Aleliūnas et al., ; Gupta & Deswal, ; Khanna & Daggard, ; Wallis, Wang, & Guerra, ). Nine replications were used for all treatments.…”