Comparative mapping of chalkiness components in rice using five populations across two environments

BACKGROUND: Chalkiness is a major constraint in rice production because it is one of the key factors determining grain quality (appearance, processing, milling, storing, eating, and cooking quality) and price. Its reduction is a major goal, and the primary purpose of this study was to dissect the genetic basis of grain chalkiness. Using five populations across two environments, we also sought to determine how many quantitative trait loci (QTL) can be consistently detected. We obtained an integrated genetic map using the data from five mapping populations and further confirmed the reliability of the identified QTL. RESULTS: A total of 79 QTL associated with six chalkiness traits (chalkiness rate, white core rate, white belly rate, chalkiness area, white core area, and white belly area) were mapped on 12 chromosomes using five populations (two doubled haploid lines and three recombinant inbred lines) across two environments (Hainan in 2004 and Wuhan in 2004). The final integrated map included 430 markers; 58.3% of the QTL clustered together (QTL clusters), 71.4% of the QTL clusters were identified in two or more populations, and 36.1% of the QTL were consistently detected in the two environments. The QTL could be detected again and showed dominance (qWBR1, qWBR8, qWBR12, and qCR5) or overdominance effects (qWCR7) for the rate of the white belly or white core, respectively, and all four QTL clusters derived from Zhenshan 97 controlling white belly rate were stably and reliably identified in an F(2) population. CONCLUSIONS: Our results identified 79 QTL associated with six chalkiness traits using five populations across two environments and yielded an integrated genetic map, indicating most of the QTL clustered together and could be detected in different backgrounds. The identified QTL were stable and reliable in the F(2) population, and they may facilitate our understanding of the QTL related to chalkiness traits in different populations and various environments, the relationships among the various chalkiness QTL, and the genetic basis for chalkiness. Thus, our results may be immediately used for map-based cloning of important QTL and in marker-assisted breeding to improve grain quality in rice breeding

Parental Selection of Hybrid Breeding Based On Maternal and Paternal Inheritance of Traits in Rapeseed (<i>Brassica napus</i> L.)

<div><p>Parental selection is crucial for hybrid breeding, but the methods available for such a selection are not very effective. In this study, a 6×6 incomplete diallel cross was designed using 12 rapeseed germplasms, and a total of 36 hybrids together with their parental lines were planted in 4 environments. Four yield-related traits and seed oil content (OC) were evaluated. Genetic distance (GD) was estimated with 359 simple sequence repeats (SSRs) markers. Heterosis levels, general combining ability (GCA) and specific combining ability (SCA) were evaluated. GD was found to have a significant correlation with better-parent heterosis (BPH) of thousand seed weight (TSW), SCA of seeds per silique (SS), TSW, and seed yield per plant (SY), while SCA showed a statistically significant correlation with heterosis levels of all traits at 1% significance level. Statistically significant correlations were also observed between GCA of maternal or paternal parents and heterosis levels of different traits except for SS. Interestingly, maternal (TSW, SS, and OC) and paternal (siliques per plant (SP) and SY) inheritance of traits was detected using contribution ratio of maternal and paternal GCA variance as well as correlations between GCA and heterosis levels. Phenotype and heterosis levels of all the traits except TSW of hybrids were significantly correlated with the average performance of parents. The correlations between SS and SP, SP and OC, and SY and OC were statistically significant in hybrids but not in parents. Potential applications of parental selection in hybrid breeding were discussed.</p></div

Phenotypic correlations between traits in hybrids and parents.

<p>The numbers in the upper or lower triangle are correlation coefficients between traits in hybrids, or between traits in parental lines.</p><p>* Significant at p = 0.05; ** significant at p = 0.01; n = 144.</p

Genetic distance between parental lines used for 6×6 incomplete diallel crosses.

<p>P1 to P6: maternal parents; P7 to P12: paternal parents.</p><p>P1, P2, P3, P7, and P8: cultivars (P1: ZS5; P2: ZS7; P3: ZS10; P7: ZS9; P8: HS5). P4 to P6, and P9 to P12: inbred lines.</p><p>See also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103165#pone.0103165.s001" target="_blank">Table S1</a> for detailed characteristics of the parental lines.</p

Heterosis level of incomplete diallel crosses.

<p>Heterosis level of incomplete diallel crosses.</p

Genetic parameters of heritability and combining ability.

<p>V_G: variance of general combining ability (GCA); V_S: variance of specific combining ability (SCA); V_gf: contribution ratio of the female GCA variance to the total variance; V_gm: contribution ratio of the male GCA variance to the total variance; V_gfm: contribution ratio of the SCA variance to the total variance; h²_b: broad sense heritability; h²_n: narrow sense heritability.</p

Correlation coefficients between GD, heterosis levels, and combining abilities of each trait.

<p>GD: genetic distance; GCA_f: GCA of female parents; GCA_m: GCA of male parents.</p><p>* Significant at p = 0.05; ** significant at p = 0.01.</p

Correlation coefficients of each trait between hybrid and its parental lines.

<p>** Significant at p = 0.01.</p

Correlation coefficients between heterosis level and average performance of parents.

<p>** Significant at p = 0.01; n = 36.</p