Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate

Abstract

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.

Keywords: Brachypodium distachyon; agronomic traits; climate change; climate simulation; ecogenomics; genome-wide association studies; genotyping; plant physiology; population genetics.

Figure 1

Distribution and genomic diversity of the B. distachyon complex. (A) Geographic distribution of 1858 Brachypodium complex accessions, classified by species: pink = B. distacyhon, blue = B. stacei, and purple = B. hybridum. (B) Population structure of the 63 diverse B. distachyon genotypes, K = 3. The three structure groups correspond to the B subgroup of B. distachyon (yellow), and the eastern (brown) and western (red) Mediterranean populations of the A subgroup of B. distachyon; and (C) geographic structure of B. distachyon across Iberian Peninsula and Turkish region. Proportions of pies represent the number of each B. distachyon subgroup (from B) at each site. The arrow from (C) to (A) shows the Australia B. distachyon (WLE2-2) and the near-identical accession from Turkey (BdTR9f).

Figure 2

Differential growth of B. distachyon under current and future climate growth temperatures. Climate chambers were used to compare the response of agronomic traits to small change in the climate for a Winter sowing in the Wagga Wagga region, south-eastern Australia. The GWAS HapMap set were grown in (A) 2015 temperature climate and (B) a 2050 temperature climate. Photos show representative plants after 16 weeks of growth. Climate chambers were programmed to have (C) diurnal and seasonal changes in temperature resulting in different rates of accumulation of thermal time (D) in the 2015 and 2050 climates. Timing of ear emergence was compared between chambers for both (E) days to ear emergence and (F) the accumulation of thermal time to ear emergence, demonstrating G × E interactions.

Figure 3

Summary of QTL for each trait under current and future climate growth temperatures. A total of 73 significant QTL were identified for a range of agronomic traits phenotyped in the 2015 temperature and 2050 temperature climates and the G × E interaction. There was little overlap between QTL for different traits but two robust QTL were identified in both environments while 16 QTL were identified for a G × E interaction. G × E, genotype by environment interaction; EarEmerg, ear emergence; TT, thermal time; PTU, photothermal units; L3Width, leaf 3 width; L3Length, leaf 3 length; GR, growth rate; GR, growth rate; EV, early vigor; phyll, phyllacron interval; AvgQY, average quantum yield; DM, dry mass; EUE, energy use efficiency

Figure 4

Putative candidate genes for QTL of key interest. (A) The ear emergence QTL, EarEmerg_QTL5.3, was significant for days to ear emergence in the 2050 temperature condition and only just under the significance threshold for the 2015 condition. Likely candidate genes include a YABBY transcription factor Bradi5g16910. (B) The early vigor QTL, EarlyVigour_QTL1.1 for leaf #3 length was found to be significant in both conditions. This region contains an ethylene sensitive transcription factor, Bradi1g00666. (C) The early vigor QTL, EarlyVigour_QTL3.1 was also identified for leaf #3 length in both environments. (D) A strong QTL was identified for photosynthetic efficiency, Energy_QTL3.2, which was significant only in the 2015 temperature condition. Likely candidate genes include a heat shock protein, Bradi3g01477, and a Low PSII Accumulation 3 (LPA3) protein, Bradi3g01550. Locus identifiers in red represent these candidate genes.