Haplotype-based genome-wide association study unveils stable genomic regions for grain yield in CIMMYT spring bread wheat

deepmala sehgal Suchismita Mondal Leonardo Abdiel Crespo Herrera Govindan Velu Philomin Juliana JULIO HUERTA_ESPINO Sandesh Kumar Shrestha Jesse Poland Ravi Singh Susanne Dreisigacker (2020, [Dataset])

Genetic architecture of grain yield (GY) has been extensively investigated in wheat using genome wide association study (GWAS) approach. However, most studies have used small panel sizes in combination with large genotypic data, typical examples of the so-called ‘large p small n’ or ‘short-fat data’ problem. Further, use of bi-allelic SNPs accentuated ‘missing heritability’ issues and therefore reported markers had limited impact in wheat breeding. We performed haplotype-based GWAS using 519 haplotype blocks on seven large cohorts of advanced CIMMYT spring bread wheat lines comprising overall 6,333 genotypes. In addition, epistatic interactions among the genome-wide haplotypes were investigated, an important aspect which has not yet been fully explored in wheat GWAS in order to address the missing heritability. Our results unveiled the intricate genetic architecture of GY controlled by both main and epistatic effects. The importance of these results from practical applications in the CIMMYT breeding program is discussed.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

Replication Data for: Genome wide association mapping for heat tolerance in sub-tropical maize

Pervez Zaidi Sudha Nair (2021, [Dataset])

Heat tolerance is becoming increasingly important for maize grown in the spring season in India because heat stress can lead to devastating yield loss. The genotypic data provided in this dataset were used to carry out GWAS analyses on 662 doubled haploid lines to identify SNPs significantly associated with several traits under normal and heat stress conditions .Haplotype blocks associated with yield contributing traits were also identified. The genomic regions detected from these analyses will require further validation before being applied in breeding pipelines..

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

Daily weather data for International Wheat Improvement Network (IWIN) locations based on AgERA5

Carlo Montes Urs Schulthess (2021, [Dataset])

Daily weather data from 1979 to 2019. The variables included are precipitation (mm), relative humidity max, relative humidity min, short wave radiation (MJ/m2/d), temperature max (°C), temperature min (°C), vapor pressure deficit max (kPa), wind speed 2m (m/s) and wind speed 10m (m/s). Data are world wide with a resolution of 0.1° x 0.1°.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

52nd International Bread Wheat Screening Nursery

Thomas Payne Ravi Singh (2020, [Dataset])

The International Bread Wheat Screening Nursery (IBWSN) is designed to rapidly assess a large number of advanced generation (F3-F7) lines of spring bread wheat under Mega-environment 1 (ME1) which represents diversity for a wide range of latitudes, climates, daylengths, fertility conditions, water management, and (most importantly) disease conditions. The distribution of these nurseries is deliberately biased toward the major spring wheat regions of the world where the diseases of wheat are of high incidence. It is distributed to 180 locations and contains 300-450 entries.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

51th International Durum Yield Nursery

Karim Ammar Thomas Payne (2020, [Dataset])

International Durum Yield Nurseries (IDYN) are replicated yield trials designed to measure the yield potential and adaptation of superior CIMMYT-bred spring durum wheat germplasm that have been developed from tests conducted under irrigation and induced stressed cropping conditions in northwest Mexico. These materials have been subjected to numerous diseases (leaf, stem and yellow rust; Septoria tritici blotch) and varied growing environments. It is distributed to 70 locations, and contains 50 entries.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

Replication Data for: Genome-wide association study of tan spot resistance in a hexaploid wheat collection from Kazakhstan

deepmala sehgal Susanne Dreisigacker (2020, [Dataset])

The genotypic data included in this dataset were generated using DArTseq by the SAGA genotyping laboratory in Mexico. The dataset contains 8,154 SNPs on candidate varieties from Kazakhstan and those released by CIMMYT-ICARDA-IWWIP program. These were evaluated for tan spot resistance at Kazakhstan.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

14th Fusarium Head Blight Screening Nursery

Pawan Singh Thomas Payne (2020, [Dataset])

The Fusarium Head Blight Screening Nursery (earlier Scab Resistance Screening Nursery - SRSN) is a single replicate nursery that contains diverse spring bread wheat (Triticum aestivum) germplasm adapted to ME2 (High rainfall environment) and ME4 (Low rainfall, semi-arid environment) with total 50-100 entries and white/red grain color.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

12th Stem Rust Resistance Screening Nursery

Ravi Singh Thomas Payne (2020, [Dataset])

The Stem Rust Resistance Screening Nursery (STEMRRSN) is a single replicate nursery that contains diverse spring bread wheat (Triticum aestivum) germplasm adapted to all mega-environments with total 50-100 entries and white/red grain color.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

8th Stem Rust Resistance Screening Nursery

Ravi Singh Thomas Payne (2020, [Dataset])

The Stem Rust Resistance Screening Nursery is a single replicate nursery that contains diverse spring bread wheat (Triticum aestivum) germplasm adapted to all mega-environments with total 50-100 entries and white/red grain color.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

10th Helminthium Leaf Blight Screening Nursery

Pawan Singh Thomas Payne (2020, [Dataset])

The Helminthium Leaf Blight Screening Nursery is a single replicate nursery that contains diverse spring bread wheat (Triticum aestivum) germplasm with total 50-100 entries and 2 REPs.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA