Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat

Abstract

We present a comprehensive survey of cytogenetic and genomic diversity of the GGA^tA^t genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement. Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGA^tA^t genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGA^tA^t genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGA^tA^t genepool. According to the results obtained, the extant GGA^tA^t genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGA^tA^t wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGA^tA^t lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGA^tA^t wheat genepool and provide the basis for an increased use of the GGA^tA^t wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.

Fig. 1

Generalized idiogram and nomenclature of the A^t- and G-genome chromosomes. The C-banding pattern is shown on the left, the pSc119.2 (red) and pAesp_SAT86 (green) pattern on the right side of each chromosome. 1–7—homoeologous groups; S—short arm, L—long arm. The numerals on the left-hand side designate putative positions of C-bands/FISH sites that can be detected on the chromosome arm; C-bands specific for the ARA-1 group are shown with pink numerals, C-bands specific for the ARA-0 group are indicated by green numerals. Red asterisks on the right-hand side indicate C-bands that were considered for the ‘chromosomal passport’

Fig. 2

Genetic relationships between GGA^tA^t and BBAA wheats. NeighborNet planar graph of Dice distances representing the diversity of 787 GGA^tA^t and BBAA tetraploid wheat genotypes based on 656 SSAP markers

Fig. 3

Natural geographic distribution of wild tetraploid T. araraticum and T. dicoccoides. Green dots correspond to collection sites of ARA-0 accessions, pink dots to ARA-1, and dark blue dots to T. dicoccoides (DIC). The collection sites of T. timopheevii and T. zhukovskyi are shown with turquoise and yellow dots, respectively. Key excavation sites in Turkey where NGW was identified are indicated with red triangles

Fig. 4

Comparison of the C-banding patterns of T. dicoccoides (DIC), T. timopheevii (TIM, a–c, normal karyotypes), T. araraticum ARA-1 (d–f) and ARA-0 (g–t). DIC (IG 117174, Gaziantep), a—KU-1818 (Georgia); b—PI 119442; c—TA1900; d—IG 116165; e—PI 654340; f—KU-1950; g—CItr 17677; h—KU-8917; i—KU-8909; j—KU-1933 (all from Turkey); k—CItr 17680 (Iran); l—PI 427381 (Erbil, Iraq); m—PI 538518; n—PI 427425 (Dahuk, Iraq); o—KU-8705; p—KU-8695 (Shaqlawa, Erbil, Iraq); q—KU-8451; r—KU-8774 (Sulaymaniyah, Iraq); s—TRI 11945 (Nakhichevan); t—KU-1901 (Armenia). 1–7—homoeologous groups. C-bands typical for ARA-1 are indicated with blue arrows, for ARA-0—with green arrows, and C-bands characteristic for T. timopheevii—with red arrows. Black arrows point to rearranged chromosomes in genotypes

Fig. 5

Chromosomal rearrangements identified in T. araraticum. The number of translocation variant corresponds to the number of the respective variant in Supplementary Table S13. Novel variants are designated with black numbers, and already known variants by red numbers

Fig. 6

Intraspecific divergence of T. araraticum and T. timopheevii. Combinations of chromosome arms in rearranged chromosomes are designated. Line colors mark the different groups: ARA-0 (green), ARA-1 (pink) and T. timopheevii (black). Solid arrows designate novel rearrangements; arrows with asterisk designate previously described rearrangements (Badaeva et al. 1990, 1994). The numerals above/next to the arrows indicate the number of accessions carrying the respective translocation

Fig. 7

Distribution of different families of tandem repeats on chromosomes of T. timopheevii and T. araraticum. Triticum timopheevii, KU-107 (a), and T. araraticum, CItr 17680, ARA-0 (b), KU-8944, ARA-0 (c), KU-1984B, ARA-1 (d), PI 427364, ARA-0 (e), and 2630, ARA-1 (f). The following probe combinations were used: a, b—pSc119.2 (green) + pTa-535 (red); d, e—pAesp_SAT86 (red) + GAA_n (green); c, f—Spelt-1 (red) + Spelt-52 (green). The position of pSc119.2 site on 1A^t chromosome typical for T. timopheevii and ARA-1 is shown with an arrow (a). Translocated chromosomes (c, d) are arrowed. Chromosomes are designated according to genetic nomenclature; the A^t-genome chromosomes are designated with yellow numerals and the G-genome chromosomes with white numerals. Scale bar, 10 µm