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Linkage disequilibrium in the euchromatic and heterochromatic genome nations

Linkage disequilibrium in the euchromatic and heterochromatic genome nations
On the lookup reported here, the level of LD try assessed into the 298 soybean germplasm accessions taken from the new USDA Soybean Germplasm Collection. Seed protein and you may oil quantity was measured inside the seeds gathered from flowers grown inside the replicated community examples from the several places. Brand new ensuing vegetables constitution study were used to check on brand new GWAS approach, and eventually to include an assessment of your own probably popularity of GWAS if it is familiar with find the fresh QTL managing the several really-understood soybean decimal faculties–vegetables proteins and you can oil articles.

Overall performance

A maximum of 30,954 SNPs distributed along the soybean genome which have slight allele frequency >0.10 and shed analysis out of below twenty five% was used to the estimate away from LD height on 298 soybean germplasm accessions. Such SNP markers spanned 950.1 Mbp, hence stands for up to 86.4% of your own step one.1 Gbp soybean genome, resulting in the typical SNP occurrence of just one SNP all 17.0 Kbp from inside the euchromatic places and you will step 1 SNP the 100.step 1 Kbp in heterochromatic countries. When you look at the euchromatic countries, new indicate number of LD mentioned from the D’ denied extremely easily to help you 0.5 within 600 Kbp, and you will suggest LD since counted because of the roentgen 2 dropped sharply in order to 0.2 at the 360 Kbp (Profile step 1). Yet not, into the heterochromatic nations, the new imply worth of D’ remained more than 0.5 until regarding 15,100 Kbp and you can indicate LD while the measured from the roentgen dos did perhaps not won’t 0.2 up until on the nine,600 Kbp (Figure step one).

The brand new suggest number of LD into the heterochromatic and you may euchromatic chromosome countries. The newest indicate LD is estimated having fun with all the sets regarding loci discover contained in this 20 Mbp off real point. Brand new X-axis suggests the length anywhere between marker sets therefore the Y-axis means LD level. The new eco-friendly and you can yellow contours correspondingly signify suggest D’ and you may mean roentgen 2 in euchromatic places, plus the bluish and purple outlines respectively signify indicate D’ and suggest r dos in heterochromatic regions.

Populace construction

All in all, 42,368 SNPs placed on the latest 20 soybean chromosomes was utilized so you can imagine the most appropriate amount (K) off subgroups in the 298 germplasm accessions. The most appropriate K value are K = 17. The accessions contained in this seven subgroups came from one Asian country and also the most other 9 subgroups was in fact comprised of a combination of accessions out-of various countries. Regarding readiness category, eight subgroups contained accessions with similar maturity classification, whereas the other 7 subgroups have been a variety of accessions out of more maturity groups.

Seeds protein and you can petroleum phenotypes

The germplasm accessions were selected based upon data in the USDA Germplasm Resources Information Network (GRIN) database ( to represent two distinct groups–one group with normal seed protein content (40 to 43%) and the other with high seed protein content (46 to 51%). However, seed protein content measured in seeds grown in replicated hill-plot trials at Beltsville, MD and Lincoln, NE showed continuous variation with a range from 35 to 50% (Figure 2A). Experimental error was low in each trial, given the coefficient of variation (CV) values of 5.77% in the MD experiment and 5.99% in the NE experiment, with an overall CV of 5.67% in the 2-location analysis. The analysis of variance indicated that the accessions differed significantly (P < 0.0001) in seed protein content, and no significant interaction between accessions and locations was detected (Table 1). The correlation coefficient (r) of seed protein concentration between the MD and NE experiments was quite high, r = 0.98 (P < 0.0001). The correlation of the accession mean seed protein measured in the NE and MD experiments with the GRIN accession protein value was moderate, r = 0.62 (P < 0.0001) and r = 0.61 (P < 0.0001), respectively. The seed oil content of the accessions displayed a pattern similar to the seed protein content relative to the GRIN oil values (Figure 2B). The analysis of variance for seed oil revealed that accessions were significantly different (P < 0.0001) and as was the case with protein, there was no significant accession ? location interaction for oil (Table 2). The correlation of accession seed oil content between the two locations was high, r = 0.95 (P < 0.0001), but was only moderately high, r = 0.77 (P < 0.0001) and r = 0.78 (P < 0.0001), between the GRIN accession values and those measured at the NE and MD locations, respectively. The correlation between mean seed protein and oil contents in the MD experiment and in the NE experiment were r = -0.64 and r = -0.66, respectively. The heritability of seed protein and seed oil concentrations was 77.9% and %, respectively. Such heritability values are higher than would be typical in breeding studies.

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