The remainder of the environmental accession material, which included the macroalgae, was examined with a stereomicroscope (Zeiss SteREO Discovery v12) in the Sherwood laboratory on Oahu and individual taxa were cleaned and preserved for molecular study (by desiccating in silica gel or freezing at −20°C) and/or isolated for culturing.
We developed markers to score a number of the SNPs across the 143 accessions (Materials and Methods) and found multiple SNPs that were shared across the population (Figure 4C).
PCA confirmed that Gypsy, as a whole superfamily, and in specific Athila and Chromovirus LTR-RTs, differed in the proximity of these elements to genes between cultivars and wild accessions (supplementary material S5, Supplementary Material online); the elements of these families were found to be close to more genes in wild than in cultivated genotypes.
We sequenced genomic DNA of the L er SRF1 locus spanning nucleotides 8982429 to 8986460 (numbers as in Col) and we sequenced full-length cDNAs obtained from mRNA isolated from L er and Col accessions (see Materials and Methods).
indica variety SHZ-2A (seeds are kindly provided by R. Mauleon, IRRI International Rice Research Institute, Los Banos, Philippines), from a pool of stigmata of the Crocus sativus L. accession "LaMancha" (material kindly provided by O. Santana-Méridas, Servicios Periféricos de Agricultura, Centro Agrario de Albaladejito, Cuenca, Spain), and from needles of Picea abies (L).
In addition to facile quality control, the core facility would enable the use of other methods to support the genotyping, such as flow cytometric estimation of ploidy level and/or genome size, keeping in mind that the genotyping data treatment differs for the diploid and polyploid accessions (see Materials and methods).
For Barke and the wild barley accessions leaf material from three to four plants was used to create bulked samples.
Synthetic coding sequences for Cxcl11aa, Cxcl11af, Cxcl11ae and Cxcl8a (included as negative control) were generated (Baseclear) according to database accessions (supplementary material Table S2).
A screen with the 20 conceptually translated Fugu proteins against the human genomic sequence database yielded 10 h/E spl)/hey-related genes (for accession numbers see Materials and Methods).
Flow cytometry protocols are used for checking ploidy among genebank accessions and breeding materials.
