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Adaptive sampling and chromosome sorting Y chromosome data

ABSTRACT: Y chromosome chromosome sorting and adaptive sampling data

PROVIDER: PRJEB58141 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
		Other
	ERR10772712.fastq.gz	Fastqsanger.gz
	ERR10772713.fastq.gz	Fastqsanger.gz
	ERR10772521.fastq.gz	Fastqsanger.gz
	ERR10772522.fastq.gz	Fastqsanger.gz

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Reducing sampling bias in molecular studies of grapevine fruit ripening: transcriptomic assessment of the density sorting method

Project description:This SuperSeries is composed of the SubSeries listed below. The interplay between environmental and genetic factors conditions the fruit ripening program in plants. Transcriptome analysis of grapevine fruits can help understanding these interactions to consciously cope with conditions leading to detrimental effects for viticultural purposes. However, considering the grapevine characteristic ripening asynchrony, which can be intensified by contrasting conditions, accurate grape sampling may be essential for molecular comparisons. In this study, berry density sorting according to floatability in NaCl solutions was assessed as a grape ripening staging strategy. Total sugar content was more correlated with berry density than with other non-invasive ripening parameters. The transcriptome was compared between three density classes collected near commercial maturity using grapevine whole-genome NimbleGen microarrays. Expression profiles clearly related with ripening progression were detected in a density series simultaneously collected from a vineyard of Albariño. By contrast, considerable differences were detected when the same density series was sampled on two different dates from the same vineyard of Tempranillo. Functional analysis indicated that environmental differences between both sampling moments determined most of these expression differences. Ripening degree-dependent responses to the environment were also detected. Finally, the effect of the sorting procedures on the grape transcriptome showed negligible when it was directly tested. Altogether, these findings evidence the convenience of homogenizing the developmental stage and the sampling time conditions for transcriptome comparisons. Berry density sorting proved useful to this end, although this method could be limited when the berry sugar concentration is not determined by the ripening developmental program.

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