Identification of QTLs Associated with Biological Nitrogen Fixation Traits in Soybean Using a Genotyping‐by‐Sequencing Approach

Abstract

2523 RESEARCH S everal legumes, when in symbiosis with bacteria collectively known as rhizobia, have the ability to assimilate atmospheric N 2 in a process called biological N fixation (BNF). Legume-rhizobia symbioses potentially contribute both to environmental and agricultural sustainability by reducing greenhouse gas emissions, nitrogenous water pollution, and fossil energy consumption (Serraj et al., 1999;Kaewsuralikhit et al., 2005;Hungria and Mendes, 2015).Soybean [Glycine max (L.) Merr.] is the most important legume cultivated worldwide. Symbiotic associations between soybean and Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, and Bradyrhizobium elkanii strains are economically and environmentally important; for example, savings on N fertilizer in Brazil with the soybean crop are estimated at about US$15 billion per cropping season (Hungria and Mendes, 2015). ABSTRACTAlthough biological N fixation (BNF) is a key process for economic cultivation of soybean [Glycine max (L.) Merr.], the trait is often neglected in breeding programs, mainly due to difficulties in evaluating nodulation and N fixation parameters. We used a genotyping-by-sequencing approach to provide a dense genome-wide marker coverage with 1448 single nucleotide polymorphisms (SNPs) distributed broadly across the chromosomes of a soybean population. The mapping population was composted of 113 F 7:8 recombinant inbred lines, obtained by singleseed descent method, derived from crossing of soybean cultivars 'Bossier' (high BNF capacity) and 'Embrapa 20' (medium BNF capacity). The traits evaluated were nodule number (NN), nodule dry weight (NDW), average NDW (ANDW; i.e., NDW/NN), and shoot dry weight (SDW). A genetic map was constructed with 1448 SNPs that generat ed 35 linkage groups totaling 1793 cM, thus covering ?72% of the genome based on the consensus linkage map. The estimated heritability for NN, NDW, ANDW, and SDW was 0.41, 0.30, 0.30, and 49.11, respectively. Inclusive composite interval mapping identified two significant quantitative trait loci (QTLs) for ANDW at 67 cM on chromosome 13, with a logarithm of odds (LOD) score of 4.66. The additive effect of this locus was −0.31 mg nodule −1 , and it explained 18.13% of the phenotypic variation. Another QTL was identified for SDW at 24 cM on chromosome 19 and exhibited an LOD score of 3.93. The additive effect was of 0.57 g plant −1 , and it accounted for 14.93% of the phenotypic variation. Additive genetic effects contribute to the final phenotype. In the present study, Embrapa 20 was the major contributor to ANDW, and Bossier was the major contributor to SDW. The latter was previously reported using simple sequence repeat markers.

Combining abilities of soybean progenies and bradyrhizobium strains for biological nitrogen fixation

“…Diverse studies conducted to evaluate the efficiency of BNF have focused on characteristics related to N assimilation capacity by the plant and to nodulation components (Arachchige et al., 2020; Grunvald et al., 2018; Hwang et al., 2014). Thus, to perform the partial diallel study, the traits N and chlorophyll contents, number of nodules, DWS, and dry weight of nodules, as well as the Z‐index, were considered.…”

“…Even though there is evidence that BNF is involved in the domestication of soybean (Munõz et al., 2016), this trait has not commonly been evaluated in breeding programs. Reports show that additive effects are predominant in inheritance of N fixation ability (Grunvald et al., 2018; Hwang et al., 2014; Santos et al., 2013; Yang et al., 2019). The results denote heritability estimates from low to high magnitude (Yang et al., 2019; Agoyi, Mohammed et al., 2016; Nicolás et al., 2002).…”

Construction of a Genetic Map of RILs Derived from Wheat (T. aestivum L.) Varieties Pamyati Azieva × Paragon Using High-Throughput SNP Genotyping Platform KASP—Kompetitive Allele Specific PCR

“…A segregating population of Recombinant Inbred Lines (RILs), was developed from a cross between the spring wheat cultivars, Pamyati Azieva (Pam) and Paragon (Par), through Single Seed Descent (SSD) bulk method (Tee and Qualset 1975) which is widely used among breeders for the last three decades (Fischer and Rebetzke 2018). RILs are a powerful tool for the mapping of genes (Broman 2005) and have been used for the identification and validation of QTL (quantitative trait loci) underpinning central agronomic traits of an important staple cereals such as wheat (Ren, Wang et al 2018), barley (Swarcewicz, Sawikowska et al 2017), rice (Ren, Wang et al 2018), chickpea (JUKTE 2018), soybean (Grunvald, Torres et al 2018) and maize (Pan, Xu et al 2017). The first parent, which is well adapted to Kazakhstan -Pamyati Azieva, used in the cross, originated from Sibirskii NIISKH in Omsk, Russia, and is widely grown in Kazakhstan because it was included into the recommended list of the State Register of the country.…”

Allelic Variants for Candidate Nitrogen Fixation Genes Revealed by Sequencing in Red Clover (Trifolium pratense L.)

“…NGS methods enable genome-wide mining of DNA polymorphisms associated with the traits analyzed. Genome-wide association studies with high-throughput genotyping by sequencing to identify loci associated with nitrogen fixation efficiency were applied in legumes such as M. truncatula [37,38] and soybean [39].…”