Author: Rajeev Varshney

Whole-genome resequencing-based QTL-seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut

Aamir W Khan Manish Pandey Rajeev Varshney (2020)

The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human-made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy-to-use genetic markers enables early-generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL-seq approach for identification of key genomic regions and candidate genes. Whole-genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta-SNP index and identified a total of 10,759 genomewide high-confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes?RING-H2 finger protein and zeaxanthin epoxidase?were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL-seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.

Article

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA ABA GENES GROUNDNUTS QUANTITATIVE TRAIT LOCI SINGLE NUCLEOTIDE POLYMORPHISM

Genomic-enabled prediction models using multi-environment trials to estimate the effect of genotype × environment interaction on prediction accuracy in chickpea

Manish Roorkiwal DIEGO JARQUIN Pooran Gaur Sandip Kale Kelly Robbins Jose Crossa Rajeev Varshney (2018)

Genomic selection (GS) by selecting lines prior to field phenotyping using genotyping data has the potential to enhance the rate of genetic gains. Genotype × environment (G × E) interaction inclusion in GS models can improve prediction accuracy hence aid in selection of lines across target environments. Phenotypic data on 320 chickpea breeding lines for eight traits for three seasons at two locations were recorded. These lines were genotyped using DArTseq (1.6 K SNPs) and Genotyping-by-Sequencing (GBS; 89 K SNPs). Thirteen models were fitted including main effects of environment and lines, markers, and/or naïve and informed interactions to estimate prediction accuracies. Three cross-validation schemes mimicking real scenarios that breeders might encounter in the fields were considered to assess prediction accuracy of the models (CV2: incomplete field trials or sparse testing; CV1: newly developed lines; and CV0: untested environments). Maximum prediction accuracies for different traits and different models were observed with CV2. DArTseq performed better than GBS and the combined genotyping set (DArTseq and GBS) regardless of the cross validation scheme with most of the main effect marker and interaction models. Improvement of GS models and application of various genotyping platforms are key factors for obtaining accurate and precise prediction accuracies, leading to more precise selection of candidates.

Article

Genotype environment interaction Forecasting Chickpeas Genomic Selection DArTseq CHICKPEA GENOMICS GENOTYPE ENVIRONMENT INTERACTION CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA

Strategies for effective use of genomic information in crop breeding programs serving Africa and South Asia

Sikiru Adeniyi Atanda Yoseph Beyene Rajeev Varshney Michael Olsen Manish Roorkiwal Manje Gowda Chellapilla Bharadwaj Pooran Gaur XUECAI ZHANG Kate Dreher Claudio César Ayala Hernández Jose Crossa Paulino Pérez-Rodríguez Abhishek Rathore Susan McCouch Kelly Robbins (2020)

Much of the world’s population growth will occur in regions where food insecurity is prevalent, with large increases in food demand projected in regions of Africa and South Asia. While improving food security in these regions will require a multi-faceted approach, improved performance of crop varieties in these regions will play a critical role. Current rates of genetic gain in breeding programs serving Africa and South Asia fall below rates achieved in other regions of the world. Given resource constraints, increased genetic gain in these regions cannot be achieved by simply expanding the size of breeding programs. New approaches to breeding are required. The Genomic Open-source Breeding informatics initiative (GOBii) and Excellence in Breeding Platform (EiB) are working with public sector breeding programs to build capacity, develop breeding strategies, and build breeding informatics capabilities to enable routine use of new technologies that can improve the efficiency of breeding programs and increase genetic gains. Simulations evaluating breeding strategies indicate cost-effective implementations of genomic selection (GS) are feasible using relatively small training sets, and proof-of-concept implementations have been validated in the International Maize and Wheat Improvement Center (CIMMYT) maize breeding program. Progress on GOBii, EiB, and implementation of GS in CIMMYT and International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) breeding programs are discussed, as well as strategies for routine implementation of GS in breeding programs serving Africa and South Asia.

Article

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA MARKER-ASSISTED SELECTION PLANT BREEDING EXPERIMENTAL DESIGN