Pollen transcriptome analysis of Solanum tuberosum (2n = 4x = 48), S. demissum (2n = 6x = 72), and their reciprocal F1 hybrids

Abstract

Pollen mRNAs were different in reciprocal F 1 hybrids, which were probably caused by a cytoplasm-nuclear chromosomal genes interaction. We have found reciprocal differences in crossability between F1 hybrids of Solanum tuberosum (T) and a Mexican wild potato species S. demissum (D). When the reciprocal hybrids were crossed as pollen parents with S. demissum, a significantly higher berry-setting rate was obtained in TD compared with DT. In this study, we performed a whole-genome transcript analysis of the pollen mRNA using a high-throughput sequencer. We obtained 12.6 billion bases that were aligned into 13,020 transcripts with 9,366 loci. All possible genetic modes were observed between the parents and their progeny, where over-dominance and under-recessive types were relatively frequent (15.7 and 15.3 %, respectively). We found that 59.1 % of transcripts were more abundant in TD and over fourfold higher transcription levels were found in 66 TD transcripts and three DT transcripts. A higher proportion of over-dominance and a lower proportion of under-recessive transcription types were also observed in TD. The percentage contributions of multiple transcripts at the same locus varied greatly and were transcribed differently between species. In the new allelic combinations created by hybridization, approximately three-fourth of the transcripts had intermediate percentage contributions between the parents but no differential transcription patterns were apparent between the reciprocal hybrids. A broad spectrum of functionally different nuclear genes was over-represented in TD pollen, some of which were directly related to pollen behavior. Since TD and DT pollen had the same composition of nuclear genes, a cytoplasm-nuclear chromosomal genes interaction is suggested for the cause of transcriptional and phenotypic differences between reciprocal hybrids.

A decade of pollen transcriptomics

“…Other species for which mature pollen transcriptome data have been published include maize (Ma et al 2008 ; Davidson et al 2011 ; Chettoor et al 2014 ), soybean (Haerizadeh et al 2009 ), grapevine (Fasoli et al 2012 ), potato (Sanetomo and Hosaka 2013 ), woodland strawberry (Hollender et al 2014 ), and most recently lily (Lang et al 2015 ).…”

Comparative Analysis of the Genetic Diversity of Chilean Cultivated Potato Based on a Molecular Study of Authentic Herbarium Specimens and Present-Day Gene Bank Accessions

“…To understand trends in genetic diversity changes in Chilean cultivars, we applied a set of commonly used markers specific to different loci of mitochondrial DNA [ 30 , 34 , 62 ] and demonstrated that all living Chilean accessions with the W-type cpDNA possessed the α-type mtDNA and the D-type cytoplasm which is characteristic for wild Mexican polyploid species, including S. demissum [ 62 , 63 , 66 ]. In addition, we showed that all living accessions with the D-type cytoplasm exhibited R1 - or R3a -gene-specific markers.…”

“…Finding the new chlorotypes within subsets of contemporary living Chilean accessions that were not detected within Chilean landraces collected in 1928 (before the late blight epidemics in Chile) might indicate genetic erosion through the introduction/introgression of genetic material from commercial varieties having in their pedigree wild species of the secondary potato gene pool. Moreover, detection of the D-type cytoplasm in living Chilean accessions typical only for Mexican polyploids [ 62 , 63 , 66 ] indicates introgression from wild Mexican species S. demissum belonging to the secondary gene pool. It is important to note that potato varieties that were developed in the 20th century represent high genetic diversity resulting from the introduction of many introgressions of wild species both from the primary and secondary potato gene pools [ 67 , 70 , 71 ].…”

Bioinformatics resources for pollen

“…Several dedicated investigations for different stages and cell types representing pollen are available (Bokvaj et al 2015;Chettoor et al 2014;Davidson et al 2011;Fasoli et al 2012;Haerizadeh et al 2009;Hafidh et al 2012;Hobo et al 2008;Hollender and Kang 2014;Lang et al 2015;Ma et al 2008;Sanetomo and Hosaka 2013;Suwabe et al 2008;Wei et al 2010). Indeed, gene expression studies by RNA-seq permitted to identify around 150 different pollen-expressed genes in different plant species associated with a range of different functions, including cell wall metabolism, cytoskeleton and signaling (Honys and Twell 2003;Palanivelu and Tsukamoto 2012;Rutley and Twell 2015).…”