Linkage Mapping and QTL Analysis of Agronomic Traits in Tetraploid Potato (Solanum tuberosum subsp. tuberosum)

Abstract

Potato (Solanum tuberosum L.) is one of the world's most important crops. Using a tetraploid population, we developed a linkage map using amplified fragment length polymorphism and simple sequence repeat (SSR) markers, and searched for quantitative trait loci (QTL) via interval mapping and single‐marker analysis of variance. Quantitative trait loci were detected for flower color, foliage maturity, tuber skin texture, dry matter content, specific gravity, and yield. Most linkage groups were anchored to Solanum chromosomes using SSRs. The most significant QTL detected was for flower color. It was located on chromosome II and explained over 40% of the variation for this trait. This QTL most likely corresponds to the R locus for red anthocyanin production. We also confirmed the presence of QTL for foliage maturity on chromosomes III and V. For skin texture, a trait that has not been previously mapped in potato, we detected multiple QTL. One of these, found on chromosome III, explained 20% of the variation. By measuring specific gravity and dry matter independently we were able to detect QTL for these traits that did not co‐locate, even though the traits are strongly correlated. Yield QTL were detected on multiple chromosomes, including a novel one on chromosome III. Many QTL could be modeled as simplex or duplex with dominant effects, but a large number displayed additive or interallelic interactive effects. The mapping and modeling of traits in this tetraploid population could be improved by the use of more codominant markers, such as single nucleotide polymorphisms.

Genetic Map and QTL Analysis of Agronomic Traits in a Diploid Potato Population using Single Nucleotide Polymorphism Markers

“…On the basis of co‐localization with QTL in diploid populations, further research using candidate gene and association mapping approaches in tetraploid populations allowed identifying diagnostic markers for superior alleles associated with tuber starch, sugar content, and yield (Draffehn et al, 2010; Gebhardt et al, 2005; Li et al, 2008; Li et al, 2005; Li et al, 2013). Linkage mapping analysis of agronomic traits in tetraploid potatoes also identified co‐localization of QTL in previous reports using diploid populations (Bradshaw et al, 2008; McCord et al, 2011a). Quantitative trait loci for yield were identified on chromosomes I, II, V, VI, VIII, and XII and for specific gravity and dry matter on chromosomes II, V, VIII, IX, and XI.…”

Development of Genetic Markers Linked to Straighthead Resistance through Fine Mapping in Rice (Oryza sativa L.)

“…Linkage mapping is a classical approach in tagging genes responsible for valuable traits and has been widely used in crops [22]–[26]. Populations that are used for linkage mapping include recombinant inbred lines (RILs), F 2 populations, backcross populations, near isogenic lines and diversity panels.…”

Genetic diversity of potato for nitrogen use efficiency under low input conditions in Ethiopia

“…Anithakumari et al (2012) in their drought tolerance study found that the same region was associated with shoot fresh weight, tuber number, tuber weight and root length under drought stress and recovery conditions. QTLs associated with foliage maturity and late blight resistance were also identified in this region under normal potato growing conditions (Visker et al, 2005;McCord et al, 2011). Khan et al (2014) in their drought tolerance study also reported that this QTL region harboured QTLs for plant height, chlorophyll content, tuber number and tuber weight under drought and well-watered conditions, indicating that the region is a potential QTL region for most important agronomic and physiological traits of potato.…”

“…QTL analysis with a wide range of molecular markers provides opportunities not only for the identification of QTLs that determine the phenotypic value of a particular trait, but also for the analysis of the relationships between traits (Lebreton et al, 1995;Simko et al, 1997). In the last two decades many QTL analysis studies have been published on different traits of potato, such as flower color, foliage maturity, tuber skin texture, dry matter content, specific gravity and yield (McCord et al,2011), yield, agronomic and quality traits (Bradshaw et al,2008), tuber yield and starch content (Schafer-Pregl et al,1998, Werij et al, 2012, tuber dormancy (van den , tuber shape (Van Eck et al, 1994b), tuber skin color (Gebhardt et al,1989), tuber flesh color (Bonierbale et al, 1988), shoot fresh weight, tuber number, tuber weight and root length under drought stress and recovery conditions (Anithakumari et al, 2011;2012) and NUE related canopy cover traits under contrasting N regimes (Ospina, 2016). However, knowledge about the genetic dissection of NUE in potato is still limited and hardly any QTL has been published for NUE and NUE related traits of potato.…”

“…In the last two decades many QTL analysis studies have been published on different traits of potato, such as flower colour, foliage maturity, tuber skin texture, dry matter content, specific gravity and yield (McCord et al, 2011), yield, agronomic and quality traits (Bradshaw et al, 2008), tuber yield and starch content (Schafer-Pregl et al, 1998), tuber dormancy (van den , tuber shape (Van Eck et al, 1994), tuber skin colour (Gebhardt et al, 1989), tuber flesh colour (Bonierbale et al, 1988) and drought related traits (Anithakumari et al, 2011(Anithakumari et al, , 2012Khan et al, 2014) .The number of QTL studies for NUE are still very limited.…”