Genotyping-by-sequencing and genomic selection applications in hexaploid triticale

Genome-wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments

Improving seed yield is one of the main targets of soybean [Glycine max (L.) Merr.] breeding. Identification of loci that influence productivity and understanding their genetic mechanism will help marker-assisted trait introgression. The present study evaluated a diverse panel of 541 soybean genotypes consisting of three maturity groups (MGs III-V) in four environments in Kansas, U.S. Data on seed yield, seed weight, shattering resistance, days to maturity, and plant height showed significant genotype, environmental, and genotype × environment interaction variations. Seed yield and shattering had moderate broad-sense heritability (<85%), while the rest of the traits showed high broad-sense heritability (>90%). The SoySNP50K iSelect BeadChip dataset was used to identify significantly associated loci via genome-wide association studies (GWAS). A total of 19 single-nucleotide polymorphisms (SNPs) were significantly associated with seed yield. Particularly, two stable seed yield quantitative trait loci (QTL) on chromosomes 9 and 17 were consistently detected in at least three out of four environments. Candidate gene analysis surrounding seed yield QTL on chromosome 9 showed that Glyma.09G048900, an oxygen binding protein, was the closest to the QTL peak. Similarly, Glyma.17G090200 and Glyma.17G090400 were within 20-kb region of the seed yield QTL on chromosome 17. The candidate genes warrant further analysis to determine their functional mechanisms and develop markers for seed yield improvement.

A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley

Barley is a diploid species with a genome smaller than those of other members of the Triticeae tribe, making it an attractive model for genetic studies in Triticeae crops. The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations. In this study, we report an ethyl methanesulfonate (EMS)-mutagenized population consisting of 8525 M₃ lines in the barley landrace "Hatiexi" (HTX), which we complement with a high-quality de novo assembly of a reference genome for this genotype. The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase, depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis. We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING (targeting induced locus lesion in genomes) platform in barley. Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals. We discovered abundant allelic mutants for dozens of genes, including the barley Green Revolution contributor gene Brassinosteroid insensitive 1 (BRI1). As a proof of concept, we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy, demonstrating the value of this resource to support forward and reverse genetic studies in barley.