Mapping and candidate gene analysis for a new top spikelet abortion mutant in rice

Grain numbers is one of the determinations for rice yield and directly associated with spikelet numbers per panicle and its normal development. Lots of genes responsible for spikelet numbers and spikelet early development have been identified, but the molecular information about the spikelet development at later development is still limited. Here, we isolated a rice spikelet abnormal development mutant, which shows degenerated spikelet at the top panicle and named aborted top spikelet mutant 1(Ats1). The spikelets derived from the middle and bottom branches per panicle of Ats1 show normal development with those of wild type. However, a large number of branches and spikelets with arrested development were often observed only on apex panicle. The abnormality did not appear until the stage In8 when rachises elongate rapidly and reproductive organs get mature, based on observations through SEM analysis. The aborted spikelet could develop the complete floral organs with a pair of rudimentary glume, a pair of empty glume, two lodicule, six stamens and one carpel. But all these floral organs did not develop maturity. Genetic analysis on two F2 populations indicated that the Ats1 was controlled by a single dominant gene. By using bulked segregant analysis of F2 population developed from Ats1 crossing with Songjing6, ATS1 was mapped on chromosome 8 between RM3819 and RM5556. Then, the fine mapping was performed with 1078 F2 population developed from Ats1 and IR36. The ATS1 locus was finely mapped in an 85.7 kb region between RM22448 and STS8-2 with 8 genes according to the rice annotation project database. Sequence analysis of the candidate genes within the delimited region of the Ats1 and Akihikari showed two-nucleotide changes, including single-nucleotide substitutions corresponding to an amino acid substitution from asparagine to lysine acid in exons 3 and a 1-bp deletion resulting in a premature stop codon in exon 22 at the candidate gene, LOC_Os08g06480. A cleaved amplified polymorphic sequence (CAPS) marker, CAPS-ats1, was developed from the 1-bp deletion site. The complete cosegregation of the CAPS genotypes with the matching phenotypes were observed in the F2 populations. This suggested that Os08g06480 is most likely the ATS1 gene. These results will provide more information for better understanding of the molecular mechanism governing top spikelet abortion within a short developmental period.