DOI: 10.5061/dryad.hmgqnk9mm
title: Alamo x Kanlow genotypic and phenotypic data for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) crosses

description: Switchgrass (Panicum virgatum L.) is a model herbaceous bioenergy crop in
 the USA. It is a native, perennial, warm-season grass, and has broad
 adaptability. Many breeding programs focus on the genetic improvement of
 switchgrass for increasing biomass yield. Significant genetic variation
 for biomass yield observed in lowland switchgrass hybrids. Due to the
 quantitative inheritance of biomass yield, varietal improvement for the
 trait through conventional breeding is slow. Therefore, quantitative trait
 loci (QTL) mapping is used to discover marker-trait associations and
 accelerate the breeding process through marker-assisted selection. To
 identify significant QTL, this study mapped seven biparental crosses and
 one combined cross of two biparental crosses (30 to 96 F1s) between
 lowland Alamo and Kanlow genotypes. The crosses were evaluated for biomass
 yield, plant height, and clonal mass scores in a simulated-sward plot with
 two replications at two locations in Tennessee from 2019 to 2021. The
 crosses were genotyped using 17,251 single nucleotide polymorphisms
 generated through genotyping-by-sequencing. QTL mapping was performed
 using a single-QTL model in R-QTL. The study identified major QTL for
 biomass yield, plant height, and clonal mass scores resided on chromosomes
 7K, 4K, and 3K and had 0.47, 0.63, and 0.62 heritability, respectively.
 The dataset contains five files describing the phenotype and genotype of
 each individual used in the quantitative trait loci (QTL) analysis. ‘File
 1’ contains biomass yield, plant height, and clonal mass data for each
 genotype and parents evaluated at two locations in Tennessee; the Plateau
 Research and Education Center (PREC), Crossville and East Tennessee
 Research and Education Center (ETREC), Knoxville from 2019 to 2021. Plant
 height and biomass yield were measured at maturity, and clonal mass scores
 were evaluated after harvesting biomass. ‘File 2’ has the genotype name,
 library, index, total reads, bases, and the Phred quality score (Q30).
 Young leaf tissue was collected from each F1 progeny and parent, and DNA
 was extracted using the cetyltrimethylammonium bromide (CTAB) procedure.
 The extracted DNA was genotyped at the USDA-ARS Western Regional Research
 Center laboratory in Albany, CA. Genotyping by sequencing (GBS) was
 performed on 951 lines (F1s and their parents) using the PstI-MspI GBS
 protocol. The quality of these sequences showed that 94.4% of the bases
 were at or above Q30. Reads were mapped to version 5.0 of the switchgrass
 reference genome. Single nucleotide polymorphism (SNP) calling was
 performed, and redundant markers were filtered out for linkage map
 construction. ‘File 3’ has SNP ID numbers, SNP locations on chromosomes,
 map positions, and SNP scores. The cross was used as a four-way cross for
 QTL analysis, where the male parent Kanlow (K) was assigned as ‘1’, and
 the female parent Alamo (A) was assigned as ‘2’. The phased output data
 from the four-way cross, i.e., 11, 12, 21, and 22, were represented by AC,
 BC, AD, and BD, respectively (‘File 3’). The progeny file (‘File 4’)
 contains the name of the parents used for making crosses and their
 progenies. A consensus linkage map (‘File 5’) was produced with Lep-Map3
 software. The linkage map contains 18 linkage groups associated with 18
 switchgrass chromosomes, marker size (bp), map position (cM) based on male
 and female maps, and map order.