Development of novel EST microsatellite markers for genetic diversity analysis and correlation analysis of velvet antler growth characteristics in Sika deer

Abstract

Background Sika deer is one of the most popular and valued animals in China. However, few studies have been conducted on the microsatellite of Sika deer, which has hampered the progress of genetic selection breeding. To develop and characterize a set of microsatellites for Sika deer which provide helpful information for protection of Sika deer natural resources and effectively increase the yield and quantity of velvet antler. Results We conducted a transcriptome survey of Sika deer using next-generation sequencing technology. One hundred eighty-two thousand two hundred ninety-five microsatellite markers were identified in the transcriptome, 170 of 200 loci were successfully amplified across panels of 140 individuals from Shuangyang Sika deer population. And 29 loci were found to be obvious polymorphic. Number of alleles is from 3 to 14. The expected heterozygosity ranged from 0.3087 to 0.7644. The observed heterozygosity ranged from 0 to 0.7698. The polymorphism information content values of those microsatellites varied ranged from 0.2602 to 0.7507. The marker-trait association was tested for 6 important and kernel characteristics of two-branched velvet antler in Shuangyang Sika deer through one-way analysis of variance. The results showed that marker-trait associations were identified with 8 different markers, especially M009 and M027. Conclusions This study not only provided a large scale of microsatellites which were valuable for future genetic mapping and trait association in Sika deer, but also offers available information for molecular breeding in Sika deer.

Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer

“…Our novel panel of 16 EST-SSRs shows high transferability and provides a reasonably high information content (0.5>PIC>0.25 and PIC>0.25, Table 2) [51]. Markers developed from ESTs show slightly lower polymorphism [31,52]. While markers with a reasonably high PIC are less informative, they can be combined with other high-information-content markers for phylogenetic analysis [53], as reported in the unweighted pair group method with arithmetic mean (UPGMA) analysis of domestic breeds [54] and the analysis of molecular variance (AMOVA) and discriminant analysis of principal components (DAPC) of papaya [55].…”

“…Transcriptome sequencing represents an effective approach for generating multiple EST sequences from nonmodel organisms [30,31]. This approach has been applied to sika deer [31,32], but EST-SSRs are still lacking for sambar, and no EST-SSR panel for deer has yet been subjected to cross-species amplification.…”

Current Situation and Utilization of Velvet Deer Germplasm Resources in China

“…They also may become the candidate genes for screening paternal individuals during breeding. Transcriptome-based EST microsatellite markers have also been developed as important DNA markers for the selection of velvet antler producing performance [ 49 , 51 ].…”