Genetic mapping of biomass yield in three interconnected Miscanthus populations

Abstract

Improving biomass yield is a major goal of Miscanthus breeding. We conducted a study on one interspecific Miscanthus sinensis 9 Miscanthus sacchariflorus F 1 population and two intraspecific M. sinensis F 1 populations, each of which shared a common parent. A field trial was established at Urbana, IL during spring 2011, and phenotypic data were collected in 2012 and 2013 for fourteen yield traits. Six high-density parental genetic maps, as well as a consensus genetic map integrating M. sinensis and M. sacchariflorus, were developed via the pseudotestcross strategy for noninbred parents with ≥1214 single-nucleotide polymorphism markers generated from restriction site-associated DNA sequencing. We confirmed for the first time a whole-genome duplication in M. sacchariflorus relative to Sorghum bicolor, similar to that observed previously for M. sinensis. Four quantitative trait locus (QTL) analysis methods for detecting marker-trait associations were compared: (1) individual parental map composite interval mapping analysis, (2) individual parental map stepwise analysis, (3) consensus map single-population stepwise analysis and (4) consensus map joint-population stepwise analysis. These four methods detected 288, 264, 133 and 109 total QTLs, which resolved into 157, 136, 106 and 86 meta-QTLs based on QTL congruency, respectively, including a set of 59 meta-QTLs common to all four analysis methods. Composite interval mapping and stepwise analysis co-identified 118 meta-QTLs across six parental maps, suggesting high reliability of stepwise regression in QTL detection. Joint-population stepwise analysis yielded the highest resolution of QTLs compared to the other three methods across all meta-QTLs. Strong, frequently advantageous transgressive segregation in the three populations indicated a promising future for breeding new higher-yielding cultivars of Miscanthus.

Winter hardiness of Miscanthus (II): Genetic mapping for overwintering ability and adaptation traits in three interconnected Miscanthus populations

“…Notably, joint‐population analyses produced significantly higher resolution for QTLs (i.e. smaller confidence intervals) than single‐population analyses, and this was consistent with our previous findings from genetic mapping for biomass yield traits (Dong, Liu, et al, ). Average confidence interval across the 31 in‐common QTLs was 27.4 ± 1.9 cM for single‐population analyses but was only 17.6 ± 1.4 cM for joint‐population analyses (Figure S1).…”

“…With joint‐population analysis, 53 QTL were detected (Figure ), whereas only 39 were detected with single‐population analyses; moreover, most of the QTL detected in single‐population analyses were also detected in the joint‐population analysis (31 in‐common QTL). Previous studies of two to ten interconnected populations have also found that joint‐population analyses identified most of the QTL identified by single‐population analyses, although each method also identified some QTLs uniquely (Chandler et al, ; Dong, Liu, et al, ; Li et al, ; Yang et al, ). Joint linkage analysis is expected to increase the power to detect QTL, and to estimate locus positions and allelic effects with greater precision than single‐population analyses (Blanc, Charcosset, Mangnin, Gallalis, & Moreau, ; Dong, Liu, et al, ; Li et al, ; Negeri, Coles, Holland, & Balint‐Kurti, ; Walling et al, ; Yang et al, ).…”

“…Spacing between and within rows was 1.5 m. In each of the field trials, the same set of 13 control genotypes, including the parents of each population, were planted; thus, the trials were analogous to locations for the control set of genotypes (but all on the same farm in close proximity to each other), and this enabled testing of genotype by trial interactions. Detailed information on population development, field trials, and management was described previously in Dong, Liu, et al ().…”

“…Genetic mapping to identify quantitative trait loci (QTLs) associated with valuable traits is a first critical step to enable marker‐assisted selection, which can be especially valuable for breeding perennial crops like Miscanthus that have multi‐year selection cycles. As Miscanthus is an obligately outcrossing species due to self‐incompatibility, genetic mapping has primarily been conducted using the pseudo‐testcross strategy on F 1 progeny (Atienza, Satovic, Petersen, Dolstra, & Martín, ; Dong, Liu, et al, ; Ge et al, ; Gifford, Chae, Swaminathan, Moose, & Juvik, ; Grattapaglia & Sederodd, ; Kim et al, ; Liu et al, ; Ma et al, ; Swaminathan et al, ; van der Weijde et al, ). However, few QTL studies on Miscanthus have been published and these have focused primarily on yield traits of M. sinensis ; to the best of our knowledge, none have been published on overwintering ability.…”

Genomics Researches and Their Applications in Plant Breeding at PAG XXIV Conference

“…These results can show the photosynthesis efficiency and chilling treatment at maturity stage. Another mapping population was generated by Dong et al (2016) …”