Genome-Wide Association Study of Nitrogen Use Efficiency and Agronomic Traits in Upland Rice

Genome-wide association study (GWAS) was performed for 16 agronomic traits including nitrogen use efficiency (NUE) and yield-related components using a panel of 190 mainly japonica rice varieties set 38 390 single nucleotide polymorphism (SNP) markers. This evaluated under rainfed upland conditions in Madagascar two consecutive cropping seasons with contrasted input levels. Using another five grain traits, we identified previously known genes (GW5, GS3, Awn1 Glabrous1), thus validating the pertinence accuracy our datasets GWAS. A total 369 significant associations were detected between SNPs gathered into 46 distinct haplotype groups 28 isolated Few signals complex quantitative trait NUE, however, larger number loci (QTLs) its component 10 2 utilization uptake efficiency, respectively. Several co-localized involved transport or remobilization within 100 kb. The present confirmed potential GWAS to identify candidate new associated traits. However, because nature NUE-related might have not captured large QTLs limited effects.