Variation in flowering time in sorghum core collection and mapping of QTLs controlling flowering time by association analysis

Yousra El Mannai 0 Tariq Shehzad 0 Kazutoshi Okuno 0 0 Y. El Mannai T. Shehzad K. Okuno (&) Lab of Plant Genetics and Breeding Science, Graduate School of Life and Environmental Sciences, University of Tsukuba , 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan A wide range of variation in flowering time was observed within a diversity research set of 107 sorghum accessions ranging from 56 to 133 days. Accessions were classified into early medium and late flowering groups. 45 accessions were grown under three different environments of photoperiod (11, 12 and 15 h). Sorghum accessions gradually responded to the decreasing of day-length. The 12 h of photoperiod could be considered as a threshold above which day-length delays the flowering time in sorghum. Association analysis was performed to identify the QTLs controlling flowering time and photoperiod sensitivity using 107 accessions of sorghum grown under natural condition and 45 accessions grown under controlled conditions. Four QTLs controlling flowering time were detected under natural condition of day-length at threshold 2.5 using K model. A total of seven flowering time loci were detected under controlled conditions of day-length. One QTL controlling photoperiod sensitivity was detected on chromosome 1 and one QTL controlling photoperiod insensitivity was detected on chromosome 4. - Flowering time is one of the essential traits determining adaptation during crop domestication. In sorghum (Sorghum bicolor (L.) Moench) flowering is considered as a crucial event because of its key role in the adaptation and geographical distribution of this crop. Flowering time is affected by environmental stimuli where photoperiod is one of the major determinant factors for this trait (Kikuchi and Handa 2009). Most of plant species exhibit some degree of photoperiodism, which is a control of the time or the date of flowering by the photoperiod. Whereas the effects of photoperiod on flowering time in sorghum are essential for the crop domestication, these effects are not well understood (Michael et al. 2008). Despite extensive analysis of the day-length control of flowering in sorghum, little is known regarding effect of variation in photoperiod or day-length on flowering time of sorghum (Menz et al. 2002). Since sorghum was recognized as short-day species by Garner and Allard (1923), photoperiod sensitivity in this species has been systematically eliminated by breeders to enlarge the range of adaptability and to extend its cropping area to temperate environment (Chanterau et al. 2001). A better understanding of response and sensitivity of flowering time in sorghum to the photoperiod will facilitate the control of flowering time. In recent years, gene mapping using linkage disequilibrium (LD) has become one of the most active areas of research in plant genetics. LD is a powerful strategy for identifying genes underlying quantitative traits in plants (Casa et al. 2008). Thus the objectives of the current study were to analyze the variation in flowering time in a diverse core set of sorghum, to explore the sensitivity of flowering time to the variation in photoperiod and to identify QTLs controlling flowering time using association analysis. Materials and methods A diversity research set of 107 sorghum accessions developed by Shehezad et al. (2009a) representing African and Asian countries was used in this study (Supplementary Table 1). According to their flowering time, accessions were divided into early, medium and late flowering groups. Fifteen accessions were randomly selected from each group. A total of 45 accessions were grown as replicated sets in three identical cabinets (at the experimental field of Tsukuba University). The day-length was set to 11, 12 and 15 h, respectively. The main effect of the photoperiod treatments was defined for each accession by counting number of days from sowing to flowering. Furthermore association analyses were conducted using the core collection grown under natural condition of day-length and the 45 accessions grown under controlled conditions to identify QTLs associated with flowering time and photoperiod sensitivity. A total of 98 markers previously described in Shehzad et al. (2009b) were used for association analyses. Population structure was performed using the program STRUCTURE version 2.2 (Pritchard et al. 2000). Bayesian clustering analyses with the admixture models were used where number of populations (J) ranged from 2 to 9. Markov chain Monte Carlo (MCMC) sampling was repeated 1 9 106 times after 1 9 104 cycles of a burn-in period. The posterior probability of J = 2 was the largest among other values and was selected after two times repetition. The Q matrix, whose (I, j)-th element was qij, was further incorporated into the association mapping models where the effect of population structure was considered. A kinship matrix, K, was calculated as allele sharing rates of the 98 SSR markers as suggested by Zhao et al. (2007) and used in the models with K effect. LD between SSR markers were estimated by D0 and r2, where D0 is the standardized disequilibrium coefficient and r2 represents the correlation between alleles at two loci. A statistical software TASSEL (Trait Analysis by Association, Evolution and Linkage) ver.2.0.1 (Bradbury et al. 2007) was used to obtain P values representing the significance of LD. To identify QTLs significantly associated with flowering time general linear model (GLM) as well as mixed linear model (MLM) were applied for analysis in TASSEL software. In GLM two different models were used (1) nave model where there is no control of population structure and kinship (2) Q model based on population structure (Yu et al. 2006). In MLM we used two models: (1) the model which accounted for kinship (K), (2) the model that takes into account both the population structure and the kinship (Q ? K). A wide range of variation in flowering time was observed within the panel of 107 sorghum accessions (Supplementary Table 1) ranging from 56 to 133 days. On the basis of number of days to flowering the 107 sorghum accessions were classified into three groups: early flowering group with less than 75 days, medium flowering from 75 to 95 days and late flowering group with more than 95 days from sowing to flowering. Under controlled conditions day-length varied substantially across experiments resulting in considerable variation in flowering time for most of the accessions from different flowering groups (Fig. 1). A photoperiod of 11 and 12 h accelerated flowering for the majority of early, medium and late accessions compared with 15 h of photoperiod. Above 12 h of photoperiod the increase of day-length generated a delay in flowering for accessions of all flowering groups. Difference in number of days to flowering between 12 and 15 h of photoperiod ranged from 4 to 18 days for the early flowering group, from 3 to 17 days in medium group and from 5 to 11 days for the late group. (...truncated)