SSR analysis of genetic changes during artificial ageing of rice seeds stored under gene bank management

Abstract

Two experiments were conducted to evaluate ageing-induced genetic changes and to establish physiological thresholds for loss of genetic integrity during ageing or storage of rice seeds. In the first experiment, seeds of 10 varieties of rice were subjected to artificial ageing in chambers conditioned to 55°C and 72±2% RH for 72 hours. In the second experiment, seeds of 4 varieties of rice stored in the NACGRAB gene bank, Nigeria in 2011 at 5± 4°C were compared with seeds of the same accessions freshly harvested in 2013. Data were collected on seed germination and seedling length to estimate the seed vigour index. Genetic changes during the ageing were evaluated by SSR markers using a Direct™ PCR kit. Genetic distance indices were computed using PAST™ software and percentage genetic integrity was estimated from the genetic distance matrices. At 72 hours of artificial ageing, seed germination percentage declined to 54.2% and vigour index 0.8 coinciding with the lowest estimate of genetic integrity of 99.5%. The decline in percentage genetic integrity during the artificial ageing indicated a systematic ageing-induced genetic alteration. SSR primer RM178 revealed variations that suggest losses of alleles in the course of ageing for 2 accessions at between 24 hours in WITA4 and 48 to 51 hours in CG14. In the gene bank storage trial, germination of seeds after one and two years of storage was above 80% and there were no significant differences among the accessions. SSR profiles for all the accessions were also similar. The result partly corroborates the artificial ageing data. This implies that seed viability benchmark of 54% is recommended for regeneration of stored rice seeds in order to maintain optimum genetic integrity during storage.

Identification and analysis of the genetic integrity of different types of rice resources through SSR markers

“…At present, lots of germplasm resources with strong viability and storability have been discovered through research on different types of germplasm resources and genetic groups. Seed viability and storability are complex quantitative traits controlled by multiple genes, and the related markers or quantitative trait locus (QTLs) are located on twelve chromosomes of rice 27 , 28 . Shigemune et al 29 investigated the effects of the QTLs for seed longevity, qLG-2 , qLG-4 and qLG-9 , using chromosome segment substitution lines.…”

Biology of Seed Vigor in the Light of -omics Tools

“…With the advent of -omics methodologies, a significant in-depth understanding of regulatory mechanisms signaling seed deterioration and invigoration has been gained and applies to crops [37,34]. Changes in specific sequences of highly polymorphic genetic markers in aging rice [38], tomatoes [39] and wheat seeds [40] provide hints of molecular hints on genetic influences behind seed aging.…”

“…From these QTL regions identified in the brief review above, putative candidate genes associated with many seed vigor traits in the hotspot QTL regions have been published for crops like Advances in Seed Biologywheat [35], maize [38] and rice [40]. Besides, Carrera et al [54] used gene expression profiling -omics method to produce a list of candidate genes that signify seed germination which was used to produce TAGGIT, a spreadsheet based seed specific gene ontology that describes the seed germination signature.…”

Research Article Evaluation of DNA integrity as a potential marker to detect aging in soybean (<i>Glycine</i> <i>max</i>) seeds

“…Gene banks are important sources of alleles to improve crops for many agronomical traits (Adeboye et al, 2015). Seed storage is the main way to conserve genetic resources of orthodox seed species since it is a low cost, efficient, reproducible and feasible method; it allows easy access to germplasm to be characterized, evaluated and used (Hawkes et al, 2000;Santos, 2006).…”