Fine Mapping of qroot-yield-1.06, a QTL for Root, Plant Vigor and Yield in Maize

Root-yield-1.06 is a major QTL affecting root system architecture (RSA) and other agronomic traits in maize. The effect of this QTL has been evaluated with the development of near isogenic lines (NILs) differing at the QTL position. The objective of this study was to fine map qroot-yield-1.06 by marker-assisted searching for chromosome recombinants in the QTL interval and concurrent root phenotyping in both controlled and field conditions, through successive generations. Complementary approaches such as QTL meta-analysis and RNA-seq were deployed in order to help prioritizing candidate genes within the QTL target region. Using a selected group of genotypes, field based root analysis by ‘shovelomics’ enabled to accurately collect RSA information of adult maize plants. Shovelomics combined with software-assisted root imaging analysis proved to be an informative and relatively highly automated phenotyping protocol. A QTL interval mapping was conducted using a segregating population at the seedling stage grown in controlled environment. Results enabled to narrow down the QTL interval and to identify new polymorphic markers for MAS in field experiments. A collection of homozygous recombinant NILs was developed by screening segregating populations with markers flanking qroot-yield-1.06. A first set of lines from this collection was phenotyped based on the adapted shovelomics protocol. QTL analysis based on these data highlighted an interval of 1.3 Mb as completely linked with the target QTL but, a larger safer interval of 4.1 Mb was selected for further investigations. QTL meta-analysis allows to synthetize information on root QTLs and two mQTLs were identified in the qroot-yield-1.06 interval. Trascriptomics analysis based on RNA-seq data of the two contrasting QTL-NILs, confirmed alternative haplotypes at chromosome bin 1.06. qroot-yield-1.06 has now been delimited to a 4.1-Mb interval, and thanks to the availability of additional untested homozygous recombinant NILs, the potentially achievable mapping resolution at qroot-yield-1.06 is c. 50 kb.

Methane production through anaerobic digestion of dedicated energy crops

Methane yield of ligno-cellulosic substrates (i.e. dedicated energy crops and agricultural residues) may be limited by their composition and structural features. Hence, biomass pre-treatments are envisaged to overcome this constraint. This thesis aimed at: i) assessing biomass and methane yield of dedicated energy crops; ii) evaluating the effects of hydrothermal pre-treatments on methane yield of Arundo; iii) investigating the effects of NaOH pre-treatments and iv) acid pre-treatments on chemical composition, physical structure and methane yield of two dedicated energy crops and one agricultural residue. Three multi-annual species (Arundo, Switchgrass and Sorghum Silk), three sorghum hybrids (Trudan Headless, B133 and S506) and a maize, as reference for AD, were studied in the frame of point i). Results exhibit the remarkable variation in biomass yield, chemical characteristics and potential methane yield. The six species alternative to maize deserve attention in view of a low need of external inputs but necessitate improvements in biodegradability. In the frame of point ii), Arundo was subjected to hydrothermal pre-treatments at different temperature, time and acid catalyst (with and without H2SO4). Pre-treatments determined a variable effect on methane yield: pre-treatments without acid catalyst achieved up to +23% CH4 output, while pre-treatments with H2SO4 catalyst incurred a methanogenic inhibition. Two biomass crops (Arundo and B133) and an agricultural residue (Barley straw) were subject to NaOH and acid pre-treatments, in the frame of point iii) and iv), respectively. Different pre-treatments determined a change of chemical and physical structure and an increase of methane yield: up to +30% and up to +62% CH4 output in Arundo with NaOH and acid pre-treatments, respectively. It is thereby demonstrated that pre-treatments can actually enhance biodegradability and subsequent CH4 output of ligno-cellulosic substrates, although pre-treatment viability needs to be evaluated at the level of full scale biogas plants in a perspective of profitable implementation.