Genetic Factors Associated With Nodulation and Nitrogen Derived From Atmosphere in a Middle American Common Bean Panel

Abstract

Among grain legume crops, common beans (Phaseolus vulgaris L.) are considered to have poor biological nitrogen (N2) fixation (BNF) capabilities although variation in N2 fixing capabilities exists within the species. The availability of genetic panel varying in BNF capacity and a large-scale single nucleotide polymorphism (SNP) data set for common bean provided an opportunity to discover genetic factors associated with N2 fixation among genotypes in the Middle American gene pool. Using nodulation and percentage of N2-derived from atmosphere (%NDFA) data collected from field trials, at least 11 genotypes with higher levels of BNF capacity were identified. Genome-wide association studies (GWASs) detected both major and minor effects that control these traits. A major nodulation interval at Pv06:28.0–28.27 Mbp was discovered. In this interval, the peak SNP was located within a small GTPase that positively regulates cellular polarity and growth of root hair tips. Located 20 kb upstream of this peak SNP is an auxin-responsive factor AUX/indole acetic auxin (IAA)-related gene involved in auxin transportation during root nodulation. For %NDFA, nitrate (NO3−) transporters, NRT1:2 and NRT1.7 (Pv02:8.64), squamosa promoter binding transcriptome factor (Pv08:28.42), and multi-antimicrobial extrusion protein (MATE) efflux family protein (Pv06:10.91) were identified as candidate genes. Three additional QTLs were identified on chromosomes Pv03:5.24, Pv09:25.89, and Pv11: 32.89 Mbp. These key candidate genes from both traits were integrated with previous results on N2 fixation to describe a BNF pathway.

Using Breeding Populations With a Dual Purpose: Cultivar Development and Gene Mapping—A Case Study Using Resistance to Common Bacterial Blight in Dry Bean (Phaseolus vulgaris L.)

“…Significant p-values were determined and set at the lowest 0.01 and 0.1% of the empirical distribution of p-values after 1,000 bootstraps were considered (Mamidi et al, 2014;Moghaddam et al, 2016;Oladzad et al, 2019aOladzad et al, ,b, 2020 and drawn as horizontal bars on the Manhattan plots. As referenced by Mamidi et al (2014) and Oladzad et al (2020), artificial cutoffs such as those from the Bonferroni test work best for traits in which only a few genetic factors are involved. For other traits, a better way to define the cutoff values is based on the trait and population.…”

“…For other traits, a better way to define the cutoff values is based on the trait and population. Bootstrapping with 1,000 resamplings "is sensitive to the fact that the more genetic factors affecting a phenotype, the corresponding values of p would be higher" (Oladzad et al, 2020). CBB resistance is a complex trait with many genetic factors affecting resistance, and thus bootstrapping with resampling provides a more applicable set of cutoff values.…”

Multi-environment Genome Wide Association Studies of Yield Traits in Common Bean (Phaseolus vulgaris L.) × Tepary Bean (P. acutifolius A. Gray) Interspecific Advanced Lines at the Humid and Dry Colombian Caribbean Subregions

“…Therefore, we used the Bonferroni threshold in order to evaluate the rate of false positives by visual interpretation of the Q–Q plots. In addition, a relax threshold of -log10 (3,196 E-4) = 3.495, as previously suggested (Pasam et al, 2012; López-Hernández and Cortés, 2019; Oladzad et al, 2019), since it is documented that the Bonferroni threshold is very restrictive or conservative in MLMs (Joo et al, 2016). Finally, the circular manhattan plots and QQplots were generated by the R-package RIdeogram (Hao et al, 2020).…”

Nodulation competitiveness and diversification of symbiosis genes in common beans from the American centers of domestication

“…To assess whether the prevalence of rhizobia reflects variation among the host, a limited number of genes that have been reported to be associated with symbiosis were examined in bean accessions from the BGD. The five bean genes were—RabA2, a small GTPase linked to a major SNP associated with nodulation 12 ; ASTRAY, a transcription factor involved in the regulation of nodulation that was found in a QTL for symbiotic nitrogen fixation 13 , 14 ; NIN ( N odule In ception, a transcription factor essential for nodulation 15 and the host nod-factor—receptor genes NFR1 and NFR5 involved in partner selection within the microsymbiont and early symbiosis-signalling pathways 16 . A release of reference genomes of acceptable quality for the Mesoamerican 17 and Andean 18 gene pools as well as for the wild beans from the Ecuadorian-Peruvian AHD regions 2 enabled us to perform comparative phylogeny among the sequences representative of that diversity as well as with orthologs from the model legumes Medicago truncatula , Lotus japonicus and Glycine max .…”

“…Sequences of five genes were examined namely gene RabA2, ASTRAY, NIN, NFR1 and NFR5. RabA2, is a gene coding for a small GTPase, associated with a major SNP for nodulation 12 ; ASTRAY, associated to a QTL linked to nodulation 13 , is a transcription factor functional in nodulation regulation 14 , NIN is a transcription factor essential for nodulation 15 , and NFR1 and NFR5, receptor proteins for rhizobia nodulation factor 16 . The nucleotide sequences of the genes NFR1 and NFR5 of accessions G21244, G21245, G23587, and G23724 were retrieved from the Sequence-Reading-File Data, available at the server of the National Center for Biotechnology Information and at accession numbers listed in SI Table 1 .…”