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Background  The effects of nutrition on testis mass in the sexually mature male have long been known, however, the cellular and molecular processes of the testis response to nutrition was not fully understood.    Methods  We tested whether the defects in spermatogenesis and increases in germ cell apoptosis in the testis that are induced by under-nutrition are associated with changes in mRNA expression and pre-mRNA alternative splicing using groups of 8 male sheep fed for a 10% increase or 10% decrease in body mass over 65 days.    Results  We identified 2,243 mRNAs, including  TP53  and  Claudin 11 , that were differentially expressed in testis from underfed and well-fed sheep (FDR < 0.1), and found that their expression changed in parallel with variations in germ cell numbers, testis size, and spermatogenesis. Furthermore, pairs of 269 mRNAs and 48 miRNAs were identified on the basis of target prediction. The regulatory effect of miRNAs on mRNA expression, in combination with functional analysis, suggests that these miRNAs are involved in abnormal reproductive morphology, apoptosis and male infertility. Nutrition did not affect the total number of alternative splicing events, but affected 206 alternative splicing events. A total of 159 genes, including  CREM ,  SPATA6 , and  DDX4 , were differentially spliced between dietary treatments, with functions related to RNA splicing and spermatogenesis. In addition, three gene modules were positively correlated with spermatogenesis-related phenotypic traits and negatively related to apoptosis-related phenotypic traits. Among these gene modules, seven ( CFLAR ,  PTPRC ,  F2R ,  MAP3K1 ,  EPHA7 ,  APP, BCAP31 ) were also differentially expressed between nutritional treatments, indicating their potential as markers of spermatogenesis or apoptosis.    Conclusions  Our findings on significant changes in mRNAs and pre-mRNA alternative splicing under-nutrition suggest that they may partly explain the disruption of spermatogenesis and the increase germ cell apoptosis. However, more research is required to verify their causal effects in regulating spermatogenesis and germ cell apoptosis.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3385-8) contains supplementary material, which is available to authorized users.

bmc genomics

Functional changes in mRNA expression and alternative pre-mRNA splicing associated with the effects of nutrition on apoptosis and spermatogenesis in the adult testis