De Novo Next Generation Sequencing of Plant Genomes

The genome sequencing of all major food and bioenergy crops is of critical importance in the race to improve crop production to meet the future food and energy security needs of the world. Next generation sequencing technologies have brought about great improvements in sequencing throughput and cost, but do not yet allow for de novo sequencing of large repetitive genomes as found in most crop plants. We present a strategy that combines cutting edge next generation sequencing with “old school” genomics resources and allows rapid cost-effective sequencing of plant genomes.     

Genome-wide association studies in a barley (Hordeum vulgare) diversity set reveal a limited number of loci for resistance to spot blotch (Bipolaris sorokiniana)

Spot blotch caused by Bipolaris sorokiniana is an important disease in barley worldwide, causing considerable yield losses and reduced grain quality. In order to identify QTL conferring resistance to spot blotch, a highly diverse worldwide barley set comprising 449 accessions was phenotyped for seedling resistance with three isolates (No 31, SH 15 and SB 61) and for adult plant resistance at two locations (Russia and Australia) in two years. Genotyping with the 50 k iSelect barley SNP genotyping chip yielded 33,818 informative markers. Genome-wide association studies (GWAS) using a compressed mixed linear model, including population structure and kinship, revealed 38 significant marker-trait associations (MTA) for spot blotch resistance. The MTA corresponded to two major QTL on chromosomes 1H and 7H and a putative new minor QTL on chromosome 7H explaining between 2.79% and 13.67% of the phenotypic variance. A total of 10 and 14 high-confidence genes were identified in the respective major QTL regions, seven of which have a predicted involvement in pathogen recognition or defence.     

New insights into genotypic thermodependency of cytoplasmic male sterility for hybrid barley breeding

The cytoplasmic male sterility (CMS) system msm1 in barley is known to be thermosensitive, sometimes resulting in spontaneous fertility restoration in the absence of the corresponding restorer gene Rfm1. Here, we investigated genotypic differences concerning temperature sensitivity and the plant developmental stage at which elevated temperature induces spontaneous fertility restoration in three CMS mother lines. While one line stayed completely male sterile, a significantly higher fertility was observed in two lines after treatment from growth stage DC 41 until maturation. Microscopic analysis revealed that sterile anthers contained neither intact pollen, nor remains of aborted pollen grains, whereas pollen was visible in anthers of potentially fertile plants. We conclude that the barley CMS system affects anther and pollen development prior to meiosis. Elevated temperature during heading and flowering can lead to a spontaneous fertility restoration by reactivating pollen growth. Nevertheless, genotypic variation exists enabling the selection for stable CMS mother lines and the development of F₁ hybrids with high hybridity. As spontaneous fertility restoration due to environmental effects is difficult to phenotype, further investigations will focus on the development of molecular markers for marker‐assisted selection.     

A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)

The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.