High density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe

Miscanthus is a bioenergy feedstock crop that has only recently become the subject of modern breeding efforts. It also has more than a 100 year history as an ornamental crop in the U.S., with many cultivars currently sold by the horticulture trade. Miscanthus is a perennial, self-incompatible, C4 grass, with some genotypes capable of maintaining high rates of photosynthesis under cold temperatures, which makes it a good choice for biomass production in the Midwestern U.S. The efficiency of breeding improved Miscanthus biomass cultivars would be greatly increased by using marker-assisted selection, because phenotypic selection for yield traits must typically be done in the second and third years of field trials. Thus, high-density genetic maps will be useful for identifying marker-trait associations that could facilitate mapping and breeding efforts in Miscanthus. Recently, a framework genetic map for M. sinensis was developed at the University of Illinois based on 658 single nucleotide polymorphism (SNP) markers using a GoldenGate genotyping array. However, sequencing of restriction site associated DNA tags (RAD-seq) is a promising approach for obtaining thousands of SNPs at lower cost than with GoldenGate. A major goal of the current research was to develop high density genetic maps of M. sinensis that integrate thousands of new RAD-seq SNPs with previously mapped but less numerous GoldenGate SNPs. In the present work, a mapping population consisted of 261 F1 progeny was developed from a cross between two diploid M. sinensis cultivars, ‘Strictus’ and ‘Kaskade’. SNP genotyping included 138 previously mapped GoldenGate SNPs and 3,044 single copy RAD tags assayed by high-throughput sequencing and called via the UNEAK pipeline in Tassel 3.0. Separate high-density genetic maps were produced for both the female parent (‘Strictus’) and the male parent (‘Kaskade’) using the regression mapping algorithm in JoinMap4.1. A composite genetic map was constructed for M. sinensis using the maximum likelihood mapping algorithm in JoinMap4.1. Zebra stripe mutants, characterized by horizontal yellow-green/white crossbands on the leaves (perpendicular to the leaf axis), have been found in many grasses, and a number of zebra stripe genes have been mapped in maize and rice. However, only one study on zebra stripe in Miscanthus has been published; a single locus model was suggested for this striping trait but it was not mapped. In the present study, segregation of zebra striping was observed in the F1 mapping population and mapped as an example to confirm the utility of the new map. Quantitative trait loci (QTL) analysis identified three QTL for zebra stripe presence/absence and three for zebra stripe intensity. Two of the zebra stripe intensity QTL may be the same as two of the zebra stripe presence/absence QTL, or tightly linked. We determined that the inheritance of the trait was recessive but incomplete penetrance was observed for each zebra stripe presence/absence QTL. Epistatic interactions were important to the expression of the trait. Three-loci models explained up to 63% of the total variation for zebra stripe presence/absence and 68% for zebra stripe intensity. Comparative mapping indicated putative correspondence between QTL detected in Miscanthus and previously cloned genes conferring zebra stripe in maize and rice