Association Genetics for Rust Resistance in Resynthesized Hexaploid Wheats and Development of their Populations through Speed Breeding

Abstract

The challenge of continuously improving the yield of wheat crop to fulfill demands of burgeoning population is challenged by several abiotic factors and diseases. Among the diseases, leaf, stripe and stem rust infections caused by Puccinia triticina f. sp. tritici, Puccinia striiformis f. sp. tritici and Puccinia graminis f. sp. tritici, respectively are considered for 20-100% production losses based on severity. The basic aim of this research was to identify and utilize the novel sources of triple rust resistance in synthetic hexaploid wheats (SHWs) created from the wild ancestors of wheat and their derivatives (SYN DERs). The artificial crossing of durum wheat genotypes (2n= 4x = 28; AABB) and Aegilops tauschii (2n = 2x = 14; DD) genotypes to create synthetic hexaploid wheat (2n = 6x = 42; BBAADD) results in the development of synthetic hexaploid wheat accessions. In our first study, we characterized 200 synthetic hexaploid wheats against all three rusts using several rust races at the seedling and the adult plant stages in Queensland, Australia. We identified 57 SHWs resistant to leaf rust, 77 to stripe rust and 69 accessions resistant to stem rust at the seedling stage. Ten accessions were resistant to all three rusts, while 32 SHWs had dual resistance against leaf and stem rusts, and 28 SHWs had dual resistance to stem and stripe rust. We identified 24 SHWs carrying adult plant resistance (APR) for leaf, stripe and stem rust. The diagnostic kompetitive allele specific PCR (KASP) molecular markers for known rust resistance genes revealed that 14 SHW accessions carried Lr34, 85 showed Lr46, and 3 SHWs showed Lr67, while none of the SHW carried Sr2. Studies for genome wide association using 50K SNP array identified 13 marker trait associations (MTAs) for stripe, stem and leaf rust resistance at the seedling plant stage. Similarly, 28 MTAs were identified for stripe, leaf and stem rust resistance at adult plant stage. The genetic resources present in SHWs cannot be directly deployed in farmer’s field due to presence of some undesirable traits. Breeders cross SHWs with adapted bread wheat cultivars to create synthetic derivatives (SYN-DERs) for transfer of gene pool of wild relatives into bread wheat. In our second study, we screened a panel of advanced wheat lines of synthetic derivatives (SYN-DERs) derived from synthetic hexaploid wheat for stripe rust resistance at the seedling and adult stage against five Pst races at two field locations i.e. Islamabad and Nowshera of Pakistan. The proportion of resistant accessions Page xiii ranged from 38% (Pst 574216) to 80% (Pst 574232) at the seedling stage, and 33% and 15% at Nowshera and Islamabad, respectively. The SYN-DER panel was genotyped with 90K SNP array and genotyping-by-sequencing (GBS) platforms respectively. GWAS identified nineteen (seedling plant resistance) and thirty seven (adult plant resistance) MTAs (marker trait associations) to stripe rust in SYN-DERs. The MTAs for adult stage resistance to stripe or yellow rust on chromosome 2D, 3D, 5D and 7D could be novel alleles and important sources for rust resistance for future breeding programs. Reduction in time for varietal improvement due to rapidly emerging environmental hazards and pathogens is dire necessity of time. In our third study we demonstrated that, newly established speed breeding technique is capable of fast generation development under controlled and light-emitting diode (LED) supplemented glasshouse. Hybridization was carried out in speed breeding glasshouse with fully controlled temperature and light conditions at The University of Queensland, Australia. This study established the rapid development of normally late maturing synthetic hexaploids and their populations, from crossing of particular parents to the next filial generations. We found that various wheat accessions (synthetic-hexaploid-wheats, landraces and bread wheat) matured in 54–64 days under speed breeding glasshouse as compared to 154 days taken under the field conditions. We attempted 236 crosses and produced healthy seeds of first filial generation in two months. Single seeds from each cross were planted and from a single plant we produced maximum 21 healthy spikes and maximum 768 healthy seeds. The speed breeding technique developed for glasshouse/chambers is better for single seed descent breeding method, particularly for wheat breeding. This breeding procedure assisted fast wheat generation development of many genotypes with healthy wheat plants and their viable seeds. Conclusively, our work identified new resistance sources to three rusts, loci underpinning resistance genes along with SNP markers and transferred resistance to adapted sources for breeding and developing mapping populations using accelerated growth method