Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value.

Sweet pepper (Capsicum annuum L.) is a high value crop and one of the most widely grown vegetables belonging to the Solanaceae family. In addition to commercial varieties and F1 hybrids, a multitude of landraces are grown, whose genetic combination is the result of hundreds of years of random, environmental, and farmer selection. High genetic diversity exists in the landrace gene pool which however has scarcely been studied, thus bounding their cultivation. We re-sequenced four pepper inbred lines, within as many Italian landraces, which representative of as many fruit types: big sized blocky with sunken apex ('Quadrato') and protruding apex or heart shaped ('Cuneo'), elongated ('Corno') and smaller sized sub-spherical ('Tumaticot'). Each genomic sequence was obtained through Illumina platform at coverage ranging from 39 to 44×, and reconstructed at a chromosome scale. About 35.5k genes were predicted in each inbred line, of which 22,017 were shared among them and the reference genome (accession 'CM334'). Distinctive variations in miRNAs, resistance gene analogues (RGAs) and susceptibility genes (S-genes) were detected. A detailed survey of the SNP/Indels occurring in genes affecting fruit size, shape and quality identified the highest frequencies of variation in regulatory regions. Many structural variations were identified as presence/absence variations (PAVs), notably in resistance gene analogues (RGAs) and in the capsanthin/capsorubin synthase (CCS) gene. The large allelic diversity observed in the four inbred lines suggests their potential use as a pre-breeding resource and represents a one-stop resource for C. annuum genomics and a key tool for dissecting the path from sequence variation to phenotype.

Número de dias e de graus-dia entre a iniciação e a diferenciação da panícula em cultivares de arroz irrigado / Number of days and degree-days between panicle initiation and panicle differentiation in irrigated rice cultivars

RESUMO: O objetivo deste trabalho foi determinar o número de dias e de graus-dia em que a iniciação da panícula (IP) antecede a diferenciação da panícula (DP) para cultivares de arroz de diferente duração de ciclo. Um experimento de campo foi conduzido em área de várzea, em Santa Maria, RS, e foi composto de três datas de semeadura e quatro cultivares ('IRGA 421', 'BRS Querência', 'IRGA 424' e 'SCSBRS Tio Taka') em dois anos agrícolas (2011/12 e 2012/13), no delineamento de blocos acaso, com quatro repetições. A data de ocorrência da DP foi estimada a partir das tabelas contidas em STEINMETZ et al. (2010) e, aproximadamente 14 dias antes da data estimada da DP, foram realizadas amostragens diárias de 10 plantas para determinar a IP em laboratório sob lupa de aumento de 45 vezes. Após a data de ocorrência da IP, 10 plantas foram coletadas diariamente para a análise da DP através do "ponto de algodão". A soma térmica foi calculada considerando a temperatura basal de 11ºC. As maiores diferenças entre as datas de ocorrência da IP e DP foram de 8 e 6 dias, e de 116,4 e 73,7ºC dia. Na maior parte dos resultados, as diferenças variaram entre 2 e 8 dias, e entre 23,8 e 116,4ºC dia. Concluiu-se que o período máximo que a IP antecede a DP é de oito dias, correspondendo a 116,4ºC dia, não sendo influenciado pela época de semeadura nem pelo comprimento de ciclo das cultivares.

ABSTRACT: The objective of this study was to determine the number of days and degree-days in which panicle initiation (PI) takes place before panicle differentiation (PD) for rice cultivars with different developmental cycle duration. A field experiment was carried out in a lowland area, in Santa Maria, RS, Brazil. The experiment consisted of three sowing dates and four rice cultivars ('IRGA 421', 'BRS Querência', 'IRGA 424' and 'SCSBRS Tio Taka') during two growing seasons (2011/12 and 2012/13), in a complete randomized block design with four replications. The date of PD was estimated from the tables contained in STEINMETZ et al. (2010) and around 14 days before the estimated date of PD. Ten plants were sampled daily to determine PI in a laboratory under a 45 times magnifying glass. After PI, 10 plants were sampled daily to determine PD using the "cotton ball" stage as a marker. Thermal sum was calculated considering the basal temperature of 11ºC. The greatest differences between the dates of occurrence between PI and PD were 8 and 6 days, and 116.4 and 73.7ºC day. Most of the differences varied between 2 and 8 days, and between 23.8 and 116.4ºC day. It was concluded that the maximum period that PI takes place before the PD is eight days, corresponding to 116.4ºC day, being influenced neither by sowing date nor by the length of cultivars cycle.