Genomic Characterization of Interspecific Hybrids and an Admixture Population Derived from Panicum amarum × P. virgatum

Abstract

Switchgrass (Panicum virgatum L.) and its relatives are regarded as top bioenergy crop candidates; however, one critical barrier is the introduction of useful genetic diversity and the development of new cultivars and hybrids. Combining genomes from related cultivars and species provides an opportunity to introduce new traits. In switchgrass, a breeding advantage would be achieved by combining the genomes of intervarietal ecotypes or interspecific hybrids. The recovery of wide crosses, however, is often tedious and may involve complicated embryo rescue and numerous backcrosses. Here, we demonstrate a straightforward approach to wide crosses involving the use of a selectable transgene for recovery of interspecific [P. virgatum cv. Alamo × Panicum amarum Ell. var amarulum or Atlantic Coastal Panicgrass (ACP)] F 1 hybrids followed by backcrossing to generate a nontransgenic admixture population. A nontransgenic herbicide-sensitive (HbS) admixture population of 83 F 1 BC 1 progeny was analyzed by genotyping-bysequencing (GBS) to characterize local ancestry, parental contribution, and patterns of recombination. These results demonstrate a widely applicable breeding strategy that makes use of transgenic selectable resistance to identify and recover true hybrids.

In situ embryo rescue for generation of wide intra‐ and interspecific hybrids of Panicum virgatum L.

“…We show that the transgenes are stably inherited and expressed using selectablable markers or reporter genes. In a previous paper (Heffelfinger et al, 2015), we showed that transgenes can be segregated to yield non-GMO hybrids in F 1 BC 1 populations. We have also used genomic analysis to confirm the identity of the parents for each F 1 offspring using the ratio of sites where neither of the two offspring alleles (transgressive events) were present in the parent compared to the total number of sites.…”

“…Genomic DNA was prepared as described in Heffelfinger et al . (). Twenty‐seven samples (eight parents and nineteen offspring) were sequenced via genotyping‐by‐sequencing (Heffelfinger et al ., ) on one Illumina Hi‐Seq 2500 lane at the Yale Center for genome analysis.…”

“…(). Twenty‐seven samples (eight parents and nineteen offspring) were sequenced via genotyping‐by‐sequencing (Heffelfinger et al ., ) on one Illumina Hi‐Seq 2500 lane at the Yale Center for genome analysis. A sample from Blackwell switchgrass was sequenced via whole‐genome sequencing on an Illumina 2000 lane.…”

“…Southern Blot and PCR analyses were carried out essentially as described in Heffelfinger et al (2015). For plants carrying the p35S-hph:Ubi R -gfp transgenes, the GFP transgene was detected via the KAPA 3G Plant PCR kit (KAPA Biosystems, Wilmington, MA) using 5 0 -ACGTAAACGGCCACAAGTTC-3 0 (forward) and 5 0 -TGCTCAGGTAGTGGTTGTCG-3 0 (reverse) primers.…”

“…This probe was used in Southern analyses of the p35S-hph:Ubi R -gfp transgenics. Transgenics generated using p35S-bar were analysed as described in Heffelfinger et al (2015).…”