Focusing the GWAS Lens on days to flower using latent variable phenotypes derived from global multienvironment trials

Abstract

Adaptation constraints within crop species have resulted in limited genetic diversity in some breeding programs and areas where new crops have been introduced, for example, for lentil (Lens culinaris Medik.) in North America. An improved understanding of the underlying genetics involved in phenology-related traits is valuable knowledge to aid breeders in overcoming limitations associated with unadapted germplasm and expanding their genetic diversity by introducing new, exotic material.We used a large, 18 site-year, multienvironment dataset phenotyped for phenologyrelated traits across nine locations and over 3 yr along with accompanying latent variable phenotypes derived from a photothermal model and principal component analysis (PCA) of days from sowing to flower (DTF) data for a lentil diversity panel (324 accessions), which has also been genotyped with an exome capture array. Genome-wide association studies (GWAS) on DTF across multiple environments helped confirm associations with known flowering-time genes and identify new quantitative trait loci (QTL), which may contain previously unknown flowering time genes. Additionally, the use of latent variable phenotypes, which can incorporate environmental data such as temperature and photoperiod as both GWAS traits and as covariates, strengthened associations, revealed additional hidden associations, and alluded to potential roles of the associated QTL. Our approach can be replicated with other crop species, and the results from our GWAS serve as a resource for further exploration into the complex nature of phenology-related traits across the major growing environments for cultivated lentil.

Evaluating the breeding potential of cultivated lentils for increasing protein and amino acid concentration in the Northern Great Plains

“…Further details about plant material and field trials can be found in Wright et al (2021). Genotyping of the LDP was done using an exome capture array, as described in previous studies (Haile et al, 2020, Neupane et al, 2023. Single nucleotide polymorphic (SNP) markers were filtered using the following criteria: (1) only biallelic markers; (2) a minor allele frequency is greater than or equal to 5%; (3) markers with a genotype missing rate less than or equal to 20%; (4) less than or equal to 20% heterozygosity.…”

Assessment of the phenotypic diversity and agronomic performance of a Mediterranean lentil collection under rainfed conditions: towards efficient use in breeding programs for adaptation to Mediterranean-type environment

“…It has been well established that phenology has played a pivotal role in the adaption of lentil to different agro-ecological regions after the spread from its center of origin (Erskine et al 1989). The dissemination of lentil from its center of origin to new agro-ecological environments has been accompanied by selection for an appropriate phenological response to regionally-speci c balance between photoperiod and temperature (Erskine et al 1994;Neupane et al 2023). The response of owering time in lentil to photoperiod has proven to be related to latitude of origin (Erskine et al 1990).…”

Assessment of the phenotypic diversity and agronomic performance of a Mediterranean lentil collection under rainfed conditions: towards efficient use in breeding programs for adaptation to Mediterranean-type environment

“…It has been well established that phenology has played a pivotal role in the adaption of lentil to different agro-ecological regions after the spread from its center of origin (Erskine et al 1989). The dissemination of lentil from its center of origin to new agro-ecological environments has been accompanied by selection for an appropriate phenological response to regionally-specific balance between photoperiod and temperature (Erskine et al 1994;Neupane et al 2023). The response of lentil flowering time to photoperiod has proven to be related to latitude of origin (Erskine et al 1990).…”