Association mapping of physiological and morphological traits related to crop development under contrasting nitrogen inputs in a diverse set of potato cultivars

Ospina Nieto, Cesar A.; Lammerts Van Bueren, Edith T.; Allefs, Sjefke; Vos, Peter G.; Linden, Gerard Van Der; Maliepaard, Chris A.; Struik, Paul C.


Ample nitrogen (N) is required for potato production, but its use efficiency is low. N supply strongly interacts with maturity type of the cultivar grown. We assessed whether variation among 189 cultivars grown with 75 or 185 kg available N/ha in 2 years would allow detecting quantitative trait loci (QTLs) for relevant traits. Using phenotypic data, we estimated various traits and carried out a genome-wide association study (GWAS) with kinship correction. Twenty-four traits and 10,747 markers based on single-nucleotide polymorphisms from a 20K Infinium array for 169 cultivars were combined in the analysis. N level affected most traits and their interrelations and influenced the detection of marker-trait associations; some were N-dependent, others were detected at both N levels. Ninety percent of the latter accumulated on a hotspot on Chromosome 5. Chromosomes 2 and 4 also contained regions with multiple associations. After correcting for maturity, the number of QTLs detected was much lower, especially of those common to both N levels; however, interestingly, the region on Chromosome 2 accumulated several QTLs. There is scope for marker-assisted selection for maturity, with the main purpose of improving characteristics within a narrow range of maturity types, in order to break the strong links between maturity type and traits like N use efficiency.