Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison

Abstract

Pre-harvest sprouting results in significant economic loss for the grain industry around the world. Lack of adequate seed dormancy is the major reason for pre-harvest sprouting in the field under wet weather conditions. Although this trait is governed by multiple genes it is also highly heritable. A major QTL controlling both pre-harvest sprouting and seed dormancy has been identified on the long arm of barley chromosome 5H, and it explains over 70% of the phenotypic variation. Comparative genomics approaches among barley, wheat and rice were used to identify candidate gene(s) controlling seed dormancy and hence one aspect of pre-harvest sprouting. The barley seed dormancy/pre-harvest sprouting QTL was located in a region that showed good synteny with the terminal end of the long arm of rice chromosome 3. The rice DNA sequences were annotated and a gene encoding GA20-oxidase was identified as a candidate gene controlling the seed dormancy/pre-harvest sprouting QTL on 5HL. This chromosomal region also shared synteny with the telomere region of wheat chromosome 4AL, but was located outside of the QTL reported for seed dormancy in wheat. The wheat chromosome 4AL QTL region for seed dormancy was syntenic to both rice chromosome 3 and 11. In both cases, corresponding QTLs for seed dormancy have been mapped in rice.

Meta-analysis of QTLs Involved in Pre-harvest Sprouting Tolerance and Dormancy in Bread Wheat

“…This region showed good synteny with terminal end of long arm of rice chromosome 3 and with the telomeric region of wheat chromosome 4AL. However, this region was located outside the QTL reported for seed dormancy in wheat on 4AL (Li et al, 2004). On the basis of available markers, the most likely position of the QTL for PHST/seed dormancy was identified in bin 4AL12-0.43-0.59 on 4AL (Li et al, 2004).…”

“…However, this region was located outside the QTL reported for seed dormancy in wheat on 4AL (Li et al, 2004). On the basis of available markers, the most likely position of the QTL for PHST/seed dormancy was identified in bin 4AL12-0.43-0.59 on 4AL (Li et al, 2004). When we compare this region with the 4AL dense map of present study, it was found that MQTL 8 (located at 75.75 cM) was present in the same region, thus suggesting the possibility of GA20-oxidase gene (TaGA20-ox1) to be a candidate for PHST/seed dormancy on 4AL.…”

“…In wheat the three homoeologues of the GA20-oxidase gene TaGA20-ox1 (involved in gibberellin biosynthesis, controlling PHST/seed dormancy) have also been mapped to chromosomes 5BL, 5DL and 4AL (Appleford et al, 2006). GA20-oxidase gene (encoding gibberellin 20 oxidase), mapped on the long arm (located in bin 4AL5-0.66-0.80) of barley chromosome 5H (Li et al, 2004) has been considered to be a candidate gene for dormancy and/or pre-harvest sprouting tolerance (PHST). This region showed good synteny with terminal end of long arm of rice chromosome 3 and with the telomeric region of wheat chromosome 4AL.…”

Barley and Wheat Share the Same Gene Controlling the Short Basic Vegetative Period

“…In this study, seven gene-specific markers were developed from six barley EST sequences using a comparative strategy, which significantly narrowed the region of the BVP-1 gene. In previous research, a comparative genomic strategy was used to identify and clone target genes in barley ( Li et al 2004;Jia et al 2009;Liu et al 2011;Ye et al 2011;Silvar et al 2012) and in wheat (Valá rik et al 2006;Kuraparthy et al 2008;Faricelli et al 2010). …”

Dormancy in cereals (not too much, not so little): about the mechanisms behind this trait

“…The major QTL for grain dormancy in wheat, which is on chromosome 4AL, explains up to 40% of the phenotypic variability in some populations. The gene underlying the QTL has not been identified but it is thought to be syntenic with the barley SD2 dormancy QTL (Li et al, 2003) on chromosome 5HL Zhang et al, 2008). The cloning of this major QTL will be an important step in providing wheat and barley breeders with new opportunities to increase dormancy in new cultivars.…”