Dynamics of senescence-related QTLs in potato

Abstract

The study of quantitative trait's expression over time helps to understand developmental processes which occur in the course of the growing season. Temperature and other environmental factors play an important role. The dynamics of haulm senescence was observed in a diploid potato mapping population in two consecutive years (2004 and 2005) under field conditions in Finland. The available time series data were used in a smoothed generalized linear model to characterize curves describing the senescence development in terms of its onset, mean and maximum progression rate and inflection point. These characteristics together with the individual time points were used in a Quantitative trait loci (QTL) analysis. Although QTLs occurring early in the senescence process coincided with QTLs for onset of senescence, the analysis of the time points made it difficult to study senescence as a continuous trait. Characteristics estimated from the senescence curve allowed us to study it as a developmental process and provide a meaningful biological interpretation to the results. Stable QTLs in the two experimental years were identified for progression rate and year-specific QTLs were detected for onset of senescence and inflection point. Specific interactions between loci controlling senescence development were also found. Epistatic interaction between QTLs on chromosomes 4, 5 and 7 were detected in 2004 and pleiotopic effects of QTLs on chromosomes 3 and 4 were observed in 2005.

Understanding the genetic basis of potato development using a multi-trait QTL analysis

“…In the E parent this QTL has a huge effect with values -log10(p) going up to 50; for most traits, the explained variances for this QTL are very high going up to 60 % for onset of senescence (Table 2). This finding is in agreement with previous reports indicating a major effect of a QTL in the same chromosomal region associated with plant maturity with pleiotropic effects on many developmental traits (Celis-Gamboa 2002;Hurtado et al 2012;Kloosterman et al 2013;Malosetti et al 2006). According to our results there is no major contribution of this QTL to the agronomic traits as indicated by the low explained variances.…”

“…In the case of flowering and senescence, early genotypes showed a complete S-shaped curve whereas late genotypes show slow progression and only the first part of the S-shape was observed in most of the genotypes. As already known, the genomic region on chromosome 5 controlling maturity has a pleiotropic effect on developmental traits (CelisGamboa 2002; Hurtado et al 2012;Malosetti et al 2006) and it can explain the curve's trajectories defined according to earliness. On the other hand, there was no clear relation between plant height and maturity as was also observed in a previous study (Maris 1964).…”

“…Single nucleotide polymorphism (SNP) markers scored in a core set of C9E (Anithakumari et al 2010) were added to the maps of parents C and E as described in Hurtado et al (2012). Together with the SNP markers, AFLP, SSR and CAPS with expected segregation ratios 1:1 and 1:1:1:1, respectively, were used to construct more saturated maps of parent C and E (additional file 1).…”

Development of a breeding strategy for nitrogen use efficiency in spinach (Spinacia oleracea L.)

“…The trials were carried out in different regions of The Netherlands with different N fertilization regimes and included organically and conventionally managed trials. Shoot biomass and canopy development were monitored throughout the crop growth period and modelled using a non-parametric approach (Hurtado et al 2012). The multi-environment dataset for curve-fitting-derived traits was used for GEI analysis as described by Malosetti et al (2013).…”

“…A smooth curve was fitted to the time series for SDW and SC to capture patterns in the data, similar to Hurtado et al (2012) using a temperature-corrected timescale. This approach allows the SDW production and SC development over the growth cycle to be described in curve descriptors that can be compared between environments even if the curves are highly divergent.…”