Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.

The purpose of this study was to characterize the varietal responses of rice (Oryza sativa L.) to N fertilization in a tropical desert climate where extremely high N application rates are needed to attain maximum yields. Eight rice cultivars of contrasting plant type and growth duration were tested at applied N levels of 0 to 480 kg N/ha in a field experiment with an intermittently flooded water regime. Among the semi‐dwarf cultivars, the earlier maturing ‘IR8x2019; produced a maximum yield of 11.7 ton/ha at 480 kg N/ha and the later maturing ‘IR5’ produced a maximum yield of 9.9 ton/ha at 400 kg N/ha. Among the tall‐statured cultivars of the traditional plant type, the earlier maturing ‘CEL 895’ produced a maximum yield of 10.6 ton/ha at 320 kg N/ha and the later maturing ‘Minabir 2’ attained its highest yield of 7.9 ton/ha at 40 kg N/ha. Yield responses to N were primarily a function of effective tillering capacity and not of panicle size. Increases in dry matter production from panicle initiation to harvest were highly correlated with grain yields. A 0.85% N content in the above‐ground parts at harvest was associated with maximum yields as well as a total N uptake of approximately 180 kg N/ha, suggesting the existence of an internal N requirement for rice in this environment. The apparent recovery of added N averaged 30%, which is considerable lower than in constantly flooded environments. The results indicate that: i) the shorter the growth duration of a cultivar within a specific plant type, the higher the yields and N response; ii) the extremely high N rates required are due to high levels of N uptake and low fertilizer recovery intermittent flooding.