Development and Evaluation of a 9K SNP Addition to the Peach Ipsc 9K SNP Array v1

The IPSC 9K peach SNP array released by the international community has been a valuable tool in research and application. Even though majority of SNPs (84%) were polymorphic in the evaluation panels there were many genomic regions with low coverage, including those important for breeding. The existing peach array has been updated with 9K additional SNPs covering previously identified gaps and including recently identified SNPs important for breeding. SNPs (1,808,996) identified by sequencing 49 genomes of additional peach accessions were used as the main source of additional SNPs. Focal point strategy was used to select 8,971 SNPs within 40kb window from the 2,821 focal points distributed across the genome. Additional 129 SNPs were chosen to saturate either regions important for breeding or close the gaps larger than 100kb. The array was validated with 1,770 peach and 26 Prunus accessions (almond, plum, apricot, wild relatives). The add-on contained 7,862 SNPs evenly spread across 8 peach pseudo-molecules with only one SNP positioned on scaffold 13 covering 224.99Mbp of peach genome. The 9K add-on improved the 9K peach array by increasing the total number of usable SNPs by 7,206. The number of SNPs per chromosome increased on average by 50% with only on average 0.18% increase in total physical coverage. Number of gaps larger than 0.3 Mbp was reduced to 2 one on each chromosome 3 and 8. Overall genotyping efficiency in all material was >90% except in almond, 82%. Number of informative markers, assessed by ASSIsT software, were highest in peach 64% and lowest in almond 10%, with 61% of markers being informative in wild Prunus (12) and 35% in apricot (4) and 2 - 33% in Japanese and European plum, respectively. Among 36.2% discarded markers 33% were monomorphic and 30% shifted homozygous in material used. Those markers could be informative in different background raising total number of informative markers. Ann addition of new SNPs to array improved the density and usefulness of the array in Prunus species. The practical applications of new 16K Illumina SNP peach array will be discussed. Specified Source(s) of Funding: USDA-NIFA-SCRI-Ros- BREED (2014-51181-22378

Genetic Variability Study in a Wide Germplasm of Domesticated Peach Through High Throughput

Peach (Prunus persica (L.) Batsch) is one of the most economically important fruit crops in temperate areas. Classical fruit tree breeding is generally slow and inefficient. Molecular markers could improve its efficiency but, although nowadays many Mendelian traits are mapped in peach and SSR markers have been found to be linked to some of the key major genes, its use in breeding programs is still limited. Main reasons for that are insufficient linkage between the markers and the genes and the lack of markers suitable for medium-high degree of multiplexing. To address this limitation, about 1,300 peach cultivars were genotyped with the 9K peach SNP chip (Verde et al. 2012) in the frame of FruitBreedomics project. This germplasm was chosen to be representative of the genetic diversity present in five germplasm collection in Europe and in China. Out of the 8144SNPs present in the chip, about 4300 were positively genotyped and used for the further analysis. The average number of heterozygous loci in the genotyped accessions was 1186 (spanning from 13 to 2775). The preliminary results of the population structure reveal three main subpopulations and the presence of high number of admixed individuals. LD seems to decay at distance longer than ca. 1 Mb. These results will be instrumental for implementing LD-based mapping of QTLs and genes in peach

Functional Role of Glutamine 28 and Arginine 39 in Double Stranded RNA Cleavage by Human Pancreatic Ribonuclease

Human pancreatic ribonuclease (HPR), a member of RNase A superfamily, has a high activity on double stranded (ds) RNA. By virtue of this activity HPR appears to be involved in the host-defense against pathogenic viruses. To delineate the mechanism of dsRNA cleavage by HPR, we have investigated the role of glutamine 28 and arginine 39 of HPR in its activity on dsRNA. A non-basic residue glycine 38, earlier shown to be important for dsRNA cleavage by HPR was also included in the study in the context of glutamine 28 and arginine 39. Nine variants of HPR respectively containing Q28A, Q28L, R39A, G38D, Q28A/R39A, Q28L/R39A, Q28A/G38D, R39A/G38D and Q28A/G38D/R39A mutations were generated and functionally characterized. The far-UV CD-spectral analysis revealed all variants, except R39A, to have structures similar to that of HPR. The catalytic activity of all HPR variants on single stranded RNA substrate was similar to that of HPR, whereas on dsRNA, the catalytic efficiency of all single residue variants, except for the Q28L, was significantly reduced. The dsRNA cleavage activity of R39A/G38D and Q28A/G38D/R39A variants was most drastically reduced to 4% of that of HPR. The variants having reduced dsRNA cleavage activity also had reduction in their dsDNA melting activity and thermal stability. Our results indicate that in HPR both glutamine 28 and arginine 39 are important for the cleavage of dsRNA. Although these residues are not directly involved in catalysis, both arginine 39 and glutamine 28 appear to be facilitating a productive substrate-enzyme interaction during the dsRNA cleavage by HPR

SK2 Channels Associate With mGlu1α Receptors and CaV2.1 Channels in Purkinje Cells

The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

Brown rot (BR) caused by Monilinia spp. leads to significant post-harvest losses in stone fruit production, especially peach. Previous genetic analyses in peach progenies suggested that BR resistance segregates as a quantitative trait. In order to uncover genomic regions associated with this trait and identify molecular markers for assisted selection (MAS) in peach, an F1 progeny from the cross "Contender" (C, resistant) 7 "Elegant Lady" (EL, susceptible) was chosen for quantitative trait loci (QTL) analysis. Over two phenotyping seasons, skin (SK) and flesh (FL) artificial infections were performed on fruits using a Monilinia fructigena isolate. For each treatment, infection frequency (if) and average rot diameter (rd) were scored. Significant seasonal and intertrait correlations were found. Maturity date (MD) was significantly correlated with disease impact. Sixty-three simple sequence repeats (SSRs) plus 26 single-nucleotide polymorphism (SNP) markers were used to genotype the C 7 EL population and to construct a linkage map. C 7 EL map included the eight Prunus linkage groups (LG), spanning 572.92 cM, with an average interval distance of 6.9 cM, covering 78.73 % of the peach genome (V1.0). Multiple QTL mapping analysis including MD trait as covariate uncovered three genomic regions associated with BR resistance in the two phenotyping seasons: one containing QTLs for SK resistance traits near M1a (LG C 7 EL-2, R2 = 13.1-31.5 %) and EPPISF032 (LG C 7 EL-4, R2 = 11-14 %) and the others containing QTLs for FL resistance, near markers SNP_IGA_320761 and SNP_IGA_321601 (LG3, R2 = 3.0-11.0 %). These results suggest that in the C 7 EL F1 progeny, skin resistance to fungal penetration and flesh resistance to rot spread are distinguishable mechanisms constituting BR resistance trait, associated with different genomic regions. Discovered QTLs and their associated markers could assist selection of new cultivars with enhanced resistance to Monilinia spp. in fruit

PEMBELAJARAN KOOPERATIF MODEL STUDENT TEAMS ACHIEVEMENT DIVISIONS (STAD) DENGAN MENERAPKAN TEORI BELAJAR BRUNNER BERBANTU JERUJI BAMBU DALAM PEMAHAMAN KONSEP PERKALIAN GUNA MENINGKATKAN HASIL BELAJAR MATEMATIKA SISWA KELAS II SDN SUMBERLESUNG 05 LEDOKOMBO JEMBER TAHUN AJARAN 2009 / 2010

Fakta di lapangan menunjukkan bahwa dalam pembelajaran masih berpusat pada guru. Siswa diam mendengarkan guru berceramah sehingga siswa pasif di dalam kelas, hal ini sangat mengurangi tanggung jawab siswa atas tugas belajarnya. Penerapan pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dapat menciptakan suasana pembelajaran yang membuat siswa aktif kreatif, menyenangkan, meningkatkan keterampilan sosial dan membantu siswa dalam memahami materi pelajaran melalui belajar secara berkelompok, sehingga diharapkan dapat meningkatkan hasil belajar. Tujuan penelitian ini adalah : (1) Untuk mengetahui pelaksanaan pembelajaran pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dalam pemahaman konsep perkalian guna meningkatkan hasil belajar matematika siswa kelas II SDN Sumberlesung 05 Ledokombo Jember tahun ajaran 2009 / 2010. (2) Untuk mengkaji aktivitas siswa pada pelaksanaan pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dalam pemahaman konsep perkalian guna meningkatkan hasil belajar matematika siswa kelas II SDN Sumberlesung 05 Ledokombo Jember tahun ajaran 2009 / 2010. (3) Untuk menganalisis ketuntasan hasil belajar pada pelaksanaan pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dalam pemahaman konsep perkalian guna meningkatkan hasil belajar matematika siswa kelas II SDN Sumberlesung 05 Ledokombo Jember tahun ajaran 2009 / 2010.. Penelitian dilaksanakan di SDN Sumberlesung 05 Ledokombo Jember, kelas II yang terdiri dari 25 orang siswa, 11 orang siswa laki-laki dan 14 orang siswa perempuan. Penelitian ini menggunakan pendekatan kualitatif. Jenis penelitiannya adalah penelitian tindakan kelas sebanyak dua siklus. Teknik pengumpulan data dengan observasi, wawancara, dan tes. Pengambilan data dilaksanakan tanggal 4 Mei 2010 sampai dengan 20 Mei 2010. Data yang dikumpulkan berupa penilaian aktivitas siswa, aktivitas guru dan skor tes. Hasil Penilaian pada siklus I pertemuan 1, aktivitas siswa mencapai 64 %, aktivitas guru 83,33 %. Pertemuan 2, aktivitas siswa mencapai 76 %, aktivitas guru 83,33 %. Siklus II pertemuan 1, aktivitas siswa mencapai 88 %, aktivitas guru 95,83 %. Pertemuan 2, aktivitas siswa mencapai 92 %, aktivitas guru 95,83 %. Analisis hasil tes akhir siklus I mencapai 84 %, dan tes akhir siklus II mencapai 92 %. Dari hasil penelitian dapat disimpulkan bahwa: 1) penerapan pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu untuk pemahaman konsep perkalian dapat menciptakan suasana pembelajaran yang membuat siswa aktif kreatif, menarik minat siswa untuk belajar, menumbuhkan kemampuan siswa dalam berinteraksi serta saling bekerja sama sehingga dapat mengembangkan keterampilan sosial siswa; 2) pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dapat meningkatkan aktivitas siswa dalam belajar. Hal ini dapat ditunjukkan pada analisis aktivitas siswa dari awal pembelajaran hingga berakhirnya pembelajaran.; 3) Ketuntasan hasil belajar siswa mengalami peningkatan, pada siklus I ketuntasan belajar secara klasikal mencapai 84 % dan pada siklus II mencapai 92 %

PEMBELAJARAN KOOPERATIF MODEL STUDENT TEAMS ACHIEVEMENT DIVISIONS (STAD) DENGAN MENERAPKAN TEORI BELAJAR BRUNNER BERBANTU JERUJI BAMBU DALAM PEMAHAMAN KONSEP PERKALIAN GUNA MENINGKATKAN HASIL BELAJAR MATEMATIKA SISWA KELAS II SDN SUMBERLESUNG 05 LEDOKOMBO JEMBER TAHUN AJARAN 2009 / 2010

Pembelajaran Kooperatif Model Student Teams Achievement Divisions (STAD) Dengan Menerapkan Teori Belajar Brunner Berbantu Jeruji Bambu Dalam Pemahaman Konsep Perkalian Guna Meningkatkan Hasil Belajar Matematika Siswa Kelas II SDN Sumberlesung 05 Ledokombo Jember Tahun Ajaran 2009/2010 : Arus Budi P, 070210204253, 2010, 50 halaman; Program Studi Pendidikan Guru Sekolah Dasar Jurusan Ilmu Pendidikan Fakultas Keguruan dan Ilmu Pendidikan Universitas Jember. Fakta di lapangan menunjukkan bahwa dalam pembelajaran masih berpusat pada guru. Siswa diam mendengarkan guru berceramah sehingga siswa pasif di dalam kelas, hal ini sangat mengurangi tanggung jawab siswa atas tugas belajarnya. Penerapan pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dapat menciptakan suasana pembelajaran yang membuat siswa aktif kreatif, menyenangkan, meningkatkan keterampilan sosial dan membantu siswa dalam memahami materi pelajaran melalui belajar secara berkelompok, sehingga diharapkan dapat meningkatkan hasil belajar. Tujuan penelitian ini adalah : (1) Untuk mengetahui pelaksanaan pembelajaran pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dalam pemahaman konsep perkalian guna meningkatkan hasil belajar matematika siswa kelas II SDN Sumberlesung 05 Ledokombo Jember tahun ajaran 2009 / 2010. (2) Untuk mengkaji aktivitas siswa pada pelaksanaan pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dalam pemahaman konsep perkalian guna meningkatkan hasil belajar matematika siswa kelas II SDN Sumberlesung 05 Ledokombo Jember tahun ajaran 2009 / 2010. (3) Untuk menganalisis ketuntasan hasil belajar pada pelaksanaan pembelajaran kooperatif model Student Teams ix Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dalam pemahaman konsep perkalian guna meningkatkan hasil belajar matematika siswa kelas II SDN Sumberlesung 05 Ledokombo Jember tahun ajaran 2009 / 2010.. Penelitian dilaksanakan di SDN Sumberlesung 05 Ledokombo Jember, kelas II yang terdiri dari 25 orang siswa, 11 orang siswa laki-laki dan 14 orang siswa perempuan. Penelitian ini menggunakan pendekatan kualitatif. Jenis penelitiannya adalah penelitian tindakan kelas sebanyak dua siklus. Teknik pengumpulan data dengan observasi, wawancara, dan tes. Pengambilan data dilaksanakan tanggal 4 Mei 2010 sampai dengan 20 Mei 2010. Data yang dikumpulkan berupa penilaian aktivitas siswa, aktivitas guru dan skor tes. Hasil Penilaian pada siklus I pertemuan 1, aktivitas siswa mencapai 64 %, aktivitas guru 83,33 %. Pertemuan 2, aktivitas siswa mencapai 76 %, aktivitas guru 83,33 %. Siklus II pertemuan 1, aktivitas siswa mencapai 88 %, aktivitas guru 95,83 %. Pertemuan 2, aktivitas siswa mencapai 92 %, aktivitas guru 95,83 %. Analisis hasil tes akhir siklus I mencapai 84 %, dan tes akhir siklus II mencapai 92 %. Dari hasil penelitian dapat disimpulkan bahwa: 1) penerapan pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu untuk pemahaman konsep perkalian dapat menciptakan suasana pembelajaran yang membuat siswa aktif kreatif, menarik minat siswa untuk belajar, menumbuhkan kemampuan siswa dalam berinteraksi serta saling bekerja sama sehingga dapat mengembangkan keterampilan sosial siswa; 2) pembelajaran kooperatif model Student Teams Achievement Divisions (STAD) dengan menerapkan teori belajar Brunner berbantu jeruji bambu dapat meningkatkan aktivitas siswa dalam belajar. Hal ini dapat ditunjukkan pada analisis aktivitas siswa dari awal pembelajaran hingga berakhirnya pembelajaran.; 3) Ketuntasan hasil belajar siswa mengalami peningkatan, pada siklus I ketuntasan belajar secara klasikal mencapai 84 % dan pada siklus II mencapai 92 %