Wheat cytogenetics in the genomics era and its relevance to breeding

Abstract

Hexaploid wheat is a species that has been subjected to most extensive cytogenetic studies. This has contributed to understanding the mechanism of the evolution of polyploids involving diploidization through genetic restriction of chromosome pairing to only homologous chromosomes. The availability of a variety of aneuploids and the ph mutants (Ph1 and Ph2) in bread wheat also allowed chromosome manipulations leading to the development of alien addition/substitution lines and the introgression of alien chromosome segments into the wheat genome. More recently in the genomics era, molecular tools have been used extensively not only for the construction of molecular maps, but also for identification/isolation of genes/QTLs (including epistatic QTLs, eQTLs and PQLs) for several agronomic traits. It has also been possible to identify gene-rich regions and recombination hot spots in the wheat genome, which are now being subjected to sequencing at the genome level, through development of BAC libraries. In the EST database also, among all plants wheat ESTs are the highest in number, and are only next to those for human, mouse, Ciona intestinalis (a chordate), rat and zebrafish genomes. These ESTs and sequences of several genomic regions have been subjected to a variety of applications including development of perfect markers and establishment of microcollinearity. The technique of in situ hybridization (including FISH, GISH and McFISH) and the development of deletion stocks also facilitated the preparation of physical maps. Molecular markers are also used for marker-assisted selection in wheat breeding programs in several countries. Construction of a wheat DNA chip, which will also become available soon, may further facilitate wheat genomics research. These enormous resources, knowledge base and the fast development of additional molecular tools and high throughput approaches for genotyping will prove extremely useful in future wheat research and will lead to development of improved wheat cultivars.

Molecular and Phenotypic Characterization of Advanced Backcross Lines Derived from Interspecific Hybridization of Durum Wheat

“…For this purpose, a large variety of wild and cultivated wheat relatives, e.g. rye, Triticum spp., Aegilops spp., Thinopyron spp., have been employed in alien introgression programs (14,19,25,30,33,37,59).…”

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

“…A variety of molecular markers including RFLPs, SSRs and AFLPs have been developed and used in this crop for different purposes including the construction of molecular maps (Somers et al 2004;Goyal et al 2005;Liu et al 2005;Song et al 2005). More recently, EST database has also been utilized in this crop for development of a variety of functional markers, particularly the EST-SSRs (Gupta & Rustgi 2004;Gupta et al 2005). An extensive study for assigning > 16 000 EST loci to chromosome bins has also been completed recently (Qi et al 2004;Peng & Lapitan 2005), although these mapped ESTs cannot be directly used as markers.…”

“…An extensive study for assigning > 16 000 EST loci to chromosome bins has also been completed recently (Qi et al 2004;Peng & Lapitan 2005), although these mapped ESTs cannot be directly used as markers. However, taken together, only ~7000 molecular markers have so far been placed on different maps (Somers et al 2004;Gupta et al 2005;Liu et al 2005;Song et al 2005;Sourdille et al 2005) although according to some estimates, as many as 10 000 to 20 000 markers are needed on one map to have a reasonably high-density map in bread wheat (Appels 2003). Therefore, keeping in view the need for developing and mapping additional markers, emphasis is now shifting to a new class of abundant markers, the single nucleotide polymorphisms (SNPs).…”

The wheat pangenome: assembly and analysis

“…Development of these resources for discovery of molecular markers was a priority in the wake of the genomics era and several projects were undertaken to build them up including the sequencing of FOSMID libraries, whole genome shotgun sequencing (Brenchley et al, 2012), sequencing of expressed sequence tags (ESTs) and the construction and sequencing of bacterial artificial chromosomes (BAC) libraries (Allouis et al, 2003(Allouis et al, , Šafář et al, 2010(Allouis et al, , Šafář et al, 2004. These new resources coupled with the extensive cytogenetic resources that have been developed since the beginning of the 20 th century have been used to improve our knowledge of the genomic architecture of wheat (Gupta et al, 2005, McFadden and Sears, 1946, Kihara, 1919, Sakamura, 1918. The ultimate goal was the construction of the complete physical map of hexaploid wheat.…”

“…Genetic mapping assays have shown that the D genome consistently has fewer markers and recombination bins , Li et al, 2015c, Sorrells et al, 2011, Semagn et al, 2006, Gupta et al, 2005, KamMorgan, 1988. It has been suggested that the little diversity found in the D genome is due to the little gene flow between the wild relative Ae.…”