Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

Abstract

Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with maintaining genetic diversity for long-term selection gains and to plan future breeding programs.

Artificial selection causes significant linkage disequilibrium among multiple unlinked genes in Australian wheat

“…This region encompasses the genes TaSus1‐7A and TaSAP1‐7A as well as a number of yield, different yield components, and quality QTL (Bennett, Izanloo, Edwards, et al, ; Bennett, Reynolds, et al, ; Maphosa et al, ; Mohler et al, ; Sukumaran, Lopes, Dreisigacker, & Reynolds, ). The average size of LD blocks in this germplasm was previously reported to be ~19 cM (Joukhadar et al, ). Thus, it is expected that selection may cause such large LD blocks in our germplasm.…”

“…F st values were averaged using a sliding window size of 15 SNPs, with a step size of one SNP. The window size was chosen considering the linkage disequilibrium and marker coverage in this germplasm, as previously described (Joukhadar et al, ). The XPCLR (Chen et al, ) scan was run with a 1 Mb grid size and 1 cM window size.…”

“…Data for this study are available at the Dryad Digital Repository: https://doi.org/10.5061/dryad.06c67 (Joukhadar, Daetwyler, Bansal, Gendall, & Hayden, ).…”

Genome-wide association analysis of stripe rust resistance loci in wheat accessions from southwestern China

“…studies. For 482 wheat cultivars from the Australian Grains Genebank, the LD estimates ranged from 19.4 cM to 27.2 cM at an r 2 value of 0.16 for cultivars from different periods (Joukhadar et al 2017). Genome-wide r 2 values declined rapidly to 0.2 within 10 cM among 43 US elite wheat cultivars and breeding lines (Chao et al 2007).…”

Population‐dependent reproducible deviation from natural bread wheat genome in synthetic hexaploid wheat

“…For example, bread wheat ( Triticum aestivum , 2 n = 6 x = 42, AABBDD) is one such major allohexaploid crop that has been reproduced artificially by crossing its ancestors ( Triticum turgidum , 2 n = 4 x = 28, AABB × Aegilops tauschii , 2 n = 2 x = 14, DD). Bread wheat has a small effective population size that is a result of its evolutionary construction and artificial selection (Kilian et al ., ; Yang et al ., ; Joukhadar et al ., , ). To fulfill the compelling need to introduce new variation from progenitor species into the cultivated gene pool, over 1500 synthetic hexaploid wheat (SHW) accessions have been developed globally (Ogbonnaya et al ., ).…”