Dissecting key biomass and adaptation traits of Miscanthus through genetic mapping, exploring mechanisms of cold tolerance, and flowering time in Miscanthus and Saccharum

Dong, Hongxu

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Description

Title

Dissecting key biomass and adaptation traits of Miscanthus through genetic mapping, exploring mechanisms of cold tolerance, and flowering time in Miscanthus and Saccharum

Author(s)

Dong, Hongxu

Issue Date

2017-11-10

Director of Research (if dissertation) or Advisor (if thesis)

Sacks, Erik J.

Doctoral Committee Chair(s)

Sacks, Erik J.

Committee Member(s)

• Juvik, John A.
• Brown, Patrick J.
• Lipka, Alexander E.

Department of Study

Crop Sciences

Discipline

Crop Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Miscanthus
• Biomass
• Adaptation
• Overwintering ability
• Flowering time
• Genetic mapping
• Genome-wide association mapping

Abstract

Improving biomass yield is a major goal of Miscanthus breeding. We conducted a study on one interspecific M. sinensis × M. sacchariflorus F1 population and two intraspecific M. sinensis F1 populations, each of which shared a common parent. A field trial was established at Urbana, IL during spring 2011, and phenotypic data was 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 pseudo-testcross strategy for non-inbred parents with ≥1,214 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 (CIM) 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. Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar M. ×giganteus (M×g) ‘1993-1780‘ in regions where average annual minimum temperatures are -26.1 C (USDA hardiness zone 5b) or lower poses a pressing need for developing new cultivars with superior cold tolerance that could be optimized for regions with severe winters. Three complementary studies on the genetics of overwintering ability of Miscanthus were conducted: 1) an interconnected population consisting of three full-sib families each with a parent in common evaluated in the field at Urbana, IL, 2) an M. sinensis germplasm panel consisting of 564 accessions evaluated in field trials at three locations in Asia and two in North America, and 3) comparison of 13 M. ×giganteus genotypes at Urbana, IL, Dixon Springs, IL, and Jonesboro, AR. By using joint population analysis of the three interconnected F1 diploid populations that shared a common parent, we identified 53 quantitative trait loci (QTLs) for nine adaptation traits, including nine overwintering ability QTLs. Negative correlations between overwintering ability and spring regrowth date and autumn dormancy date suggested that the genotypes most likely to survive winters were those that emerged early in spring and/or went dormant early in autumn. From genome-wide association analyses (GWA) of the germplasm panel study, we detected 73 marker-trait associations for overwintering ability. We found that Korea/N China M. sinensis genetic group could be a valuable gene pool for cold tolerance. The M. sinensis Yangtze-Qinling, Southern Japan and Northern Japan genetic groups were also potential sources of cold-tolerance. Comparisons between QTL analyses and GWA analyses, we found two overwintering ability QTLs that corresponded to seven GWA hits. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold-responsive gene, COR47. The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and two known cold stress related genes, carboxylesterase 13 (CEX13) and WRKY transcription factor (WRKY2). The QTL on LG 11 was also surrounded by one cold shock domain (CDSP1). Many biologically intuitive candidate genes were observed within or near the QTLs and GWA hits detected in this study, suggesting their validity and potential for further study. From the comparison of 13 M×g genotypes at three US locations, we identified several genotypes with superior cold tolerance to the commercial cultivar ‘1993-1780‘, suggesting a promising future for improving adaptation in Miscanthus. Miscanthus is a close relative of Saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between Miscanthus and Saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of Saccharum and Miscanthus genotypes. We found that day length was an important factor influencing when Miscanthus and Saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d-1, which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 Miscanthus genotypes, including 28 M. sinensis, 2 M. floridulus, and 3 M. ×giganteus collected from 20.91° S to 44.92° N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted M. sinensis flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for M. sinensis and M. floridulus from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-day treatments and the 15 h day treatment. Under short days, short culms for high-latitude accessions was achieved by different physiological mechanisms for M. sinensis genetic groups from the mainland in comparison to those from Japan; for mainland accessions, the mechanism was reduced internode length, whereas for Japanese accessions the phyllochron under short days was greater than under long days. Thus, for M. sinensis, short days typically hastened floral induction, consistent with expectations for a facultative short-day plant. However, for high latitude accessions of M. sinensis, days less than 12.5 h also signaled that plants should prepare for winter by producing many short culms with limited elongation and development; moreover, this response was also epistatic to flowering. Thus, to flower M. sinensis that originates from high latitudes synchronously with sugarcane, the former needs day lengths >12.5 h (perhaps as high as 15 h), whereas the latter needs day lengths <12.5 h.

Graduation Semester

2017-12

Type of Resource

text

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Copyright 2017 Hongxu Dong

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