Genomic DNA Extraction and Sequencing of F2 Pumpkin Pools

Total genomic DNA was extracted from fresh leaves of young seedlings using the CTAB method (VWI, China) as described in Liao et al. [41 (link)]. The F₂ offspring H-pool (hulled pumpkins) and HL-pool (hull-less pumpkins) were constructed by mixing 40 hulled and 40 hull-less F₂ individuals. A TruSeq Nano DNA LT Sample Prep Kit (Illumina, USA) was used to construct sequencing libraries. All libraries were sequenced on an Illumina HiSeq 4000 platform. The sequencing data quality was determined by FASTQC [55 (link)]. The QC standard pipelines were employed as described in Liao et al [41 (link)].

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Lyu X., Shi L., Zhao M., Li Z., Liao N., Meng Y., Ma Y., Zhou Y., Xue Q., Hu Z., Yang J, & Zhang M. (2022). A natural mutation of the NST1 gene arrests secondary cell wall biosynthesis in the seed coat of a hull-less pumpkin accession. Horticulture Research, 9, uhac136.

Publication 2022

TruSeq Nano DNA LT Sample Prep Kit HiSeq 4000 platform

Ctab Genomic Pumpkins Seedlings

Corresponding Organization : Ministry of Agriculture and Rural Affairs

Top 5 similar protocols

Variable analysis

independent variables

Presence of hull in F2 offspring (hulled vs. hull-less pumpkins)

dependent variables

Sequencing data quality

control variables

Fresh leaves of young seedlings
CTAB method for DNA extraction
TruSeq Nano DNA LT Sample Prep Kit for library construction
Illumina HiSeq 4000 platform for sequencing

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