Chromosome diversity and its effects in wheat landraces from Shanxi province, China

Chromosome variation plays a crucial role in the evolution of bread wheat. To explore chromosome diversity and its potential effects, high-resolution karyotypes of 152 Shanxi wheat landraces were developed and compared using oligonucleotide fluorescence in situ hybridization (Oligo-FISH). The genetic effects of different chromosomal variations on agronomic traits were also evaluated. The results revealed extensive chromosomal diversity, including 15 structural variations, one chromosomal number variation, and 108 polymorphic chromosome blocks, which were associated with 59 presence/absence variations (PAVs) and 25 copy number variations (CNVs). Chromosomal translocations were detected in all chromosomes except 5B of the B subgenome, which also exhibited the highest proportion of variations (56.7%). A subgenome showed the greatest number of polymorphic types (50), along with the highest polymorphism information content (PIC) value, followed by the B and D subgenomes. Chromosomal PIC, genetic diversity, and genetic distance were influenced by genetic relationships and the ecological distribution of the germplasm. Cluster analysis based on genetic distance grouped all accessions into eight distinct categories. Chromosomal variation types differed across wheat production regions, and landraces with the same name often displayed divergence in both chromosomal variation types and polymorphism levels, further supported by genetic differences revealed through 0.1K and 16K SNP chips. Agronomic traits in the Shanxi wheat landraces also showed considerable variation, with coefficients of variation (CVs) ranging from 6.33% to 32.95%. Except for spike length, uppermost internode and grain number per spike, the higher CVs and genetic diversity for each trait were observed in the northern spring wheat-growing region. Twenty-two chromosomal variations were associated with agronomic traits. Notably, PAV.2A-g1 significantly increased spike length; both PAV.2A-g1 and PAV.2B-r8 positively influenced spikelet number per spike; and PAV.6A-g6 and PAV.6B-g11 were associated with grain weight. These findings underscore the potential application of these variations in wheat improvement and provide valuable insights into the genetic diversity of Shanxi wheat landraces, offering novel marker types for molecular marker-assisted breeding.