Genetic interaction involving photoperiod-responsive Hd1 promotes early flowering under long-day conditions in rice (original) (raw)
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Photoperiodic control of flowering is one of the most significant components of the interaction between plants and their environment. Hd1 promotes floral transition from vegetative to reproductive growth under short-day (SD) conditions. An indel-specific functional marker in Hd1 first exon was developed and tested in a collection of 44 rice indica cultivars with different flowering times to evaluate its association with the trait. Results showed that the Hd1 indel-specific marker produced three allelic forms A, B and C as expected, with frequencies of 43.2, 47.7 and 9.1 percent, respectively. A high negative correlation (r=-0.556) was detected between flowering time and functional Hd1 indel. Interval mapping (IM) analysis showed that Hd1 had a negative additive effect (~4.5 days) on flowering time and the gene explained 27.4 percent of phenotypic variation of the trait. Our results indicated the role of Hd1 in determining the time of flowering in rice and suggest applicability of Hd1 indel-specific marker in molecular breeding of early flowering.
2020
Background Plant domestication/adaptation is a good model for evo-devo studies. Mutations that caused morphological and physiological change, followed by human selection, finally led to improvement of phenotypes suitable for different kinds of environments. Originating from the Yangtze Valley, rice is a facultative short-day plant. Rice spread southward thousands of years ago, but one of the new traits beneficial to crop yield would be loss of sensitivity to photoperiod. That is, if rice could be cultivated 2 or 3 seasons each year, the production would at least double. Results We used the sequence information for Heading date 1 (Hd1) gene to reveal the relationship of sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes were reported previously. By data mining the genome sequencing information in the public domain, we discovered another 3 types. Allele haplotypes are present in sub-tropical and tropical regions, which indicat...
International Journal of Molecular Sciences
Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS5...