QTL Analysis of Symbiotic Nitrogen Fixation in a Black Bean Population

Abstract

L egumes in symbiosis with soil rhizobia are reported to fix 20 to 22 million Mg of nitrogen (N) each year in agricultural production systems (Herridge et al., 2008). Large differences exist in the proportion of atmospheric N 2 fixed by grain legume crops, and common (dry) bean (Phaseolus vulgaris L.) is among the lowest in symbiotic N fixation (SNF). For example, 75% of the total N in a faba bean (Vicia faba L.) plant was derived through SNF; 62 to 94% of N in soybean [Glycine max (L.) Merr.], pea (Pisum sativum L.), and lentil (Lens culinaris Medikus); 54 to 58% of N in cowpea [Vigna ungiculata (L.) Walp.], chickpea (Cicer arietanum L.), and pigeon pea [Cajanus cajan (L.) Millsp.]; and 39% of N in common bean (Dwivedi et al., 2015). The percentage of nitrogen derived from the atmosphere (Ndfa) fixed by dry bean is also quite variable depending on genotype and environmental conditions. Using the 15 N natural abundance method, Farid et al., (2016) reported an average 28% Ndfa in low-N environments. Pereira et al. (1989) also reported an average Ndfa of 21.6%, but cultivars ranged from 5.7% for the navy bean 'Sanilac' to 31.6% for the black bean landrace 'Puebla 152'. A weak relationship ABSTRACT Dry bean (Phaseolus vulgaris L.) acquires nitrogen (N) from the atmosphere through symbiotic N fixation (SNF) but is considered a poor N fixer. Diversity for SNF within dry bean germplasm is recognized, and regions of the genome associated with SNF traits have recently been identified. In the current study a mapping population of 122 recombinant inbred lines (rILs), derived from the cross of two black bean cultivars ('puebla 152' and 'Zorro') contrasting in SNF traits, was grown in the field in East Lansing, MI, and Isabela, puerto rico, and in the greenhouse under N-free conditions to evaluate for yield, nodule development, biomass growth, agronomic traits, and N fixation. The rIL population was also genotyped with single-nucleotide polymorphism (SNp) markers developed through the BeanCAp to construct a genetic map spanning 972 cM and containing 430 SNps. A total of 17 unique QTL associated with SNF traits were identified with most of them located in three large clusters on pv01 (4), pv06 (6), and pv08 (6). Many of the QTL associated with %N derived from atmosphere, N harvest index, and %N in biomass were also associated with candidate genes expressed in the nodules and roots. The majority of QTL associated with genes expressed in the root or nodule were derived from puebla 152, while QTL associated with genes with enhanced expression in stems and pods were associated with Zorro. The QTL described should serve as potential targets for improvement of SNF characteristics in commercial dry bean genotypes adapted to temperate zones.

Identification of QTL Associated with Drought Tolerance in Andean Common Bean

“…This was consistent with several previous studies that reported QTL for yield on Pv03 (Wright and Kelly, 2011;Checa and Blair, 2012;Mukeshimana et al, 2014;Hoyos-Villegas et al, 2015;Kamfwa et al, 2015;Heilig et al, 2017). In addition, two separate studies mapped SY3.3 on Pv03 near markers ss715639345 (39.6 Mb) and ss715646621 (39.4 Mb) in a Middle American Puebla 152 ´ Zorro black bean population (Heilig et al, 2017). Yield QTL YLD3.1 GG and YLD3.2 GG linked to markers BM197 and AG01, respectively, were reported in a G2333 ´ g19839 population in Popayán (Checa and Blair, 2012), and QTL YLD3.1 DB , YLD3.2 DB , YLD3.3 DB , and YLD3.4 DB near markers AE103, Q1001, BM181, and AD1801, respectively, were detected on Pv03 under NS conditions in a DOR 364 ´ BAT 477 population .…”

“…SY3.3 PR had a LOD of 3.45 and additive allelic effect of 2.38 g, explaining 9.7% of variation in SY under DS. This was consistent with several previous studies that reported QTL for yield on Pv03 (Wright and Kelly, 2011;Checa and Blair, 2012;Mukeshimana et al, 2014;Hoyos-Villegas et al, 2015;Kamfwa et al, 2015;Heilig et al, 2017). The QTL YLD3.1 CG linked to marker BM172 and YLD3.2 CG near marker BM98 for yield were reported in Popayán using an ICA Cerinza ´ G 24404 population .…”

Identification of a gene encoding a sugar transporter as a potential target of a novel LysR‐type transcriptional regulator rluD from rhizobium required for symbiotic nodulation in soybean (Glycine max Merr.)

“…Although several studies have reported mapping nodulation‐related traits or biological nitrogen fixation traits in legumes, the candidate genes that are most likely involved in symbiotic nodulation have not been studied (Diaz et al., ; Heilig et al., ; Kamfwa et al., ). The candidate genes for nodule‐related QTLs that were confirmed and cloned were Rfg1 , Rj2 and Rj4 (Tang et al., ; Tsurumaru et al., ), which were a variety of dominant genes shown to restrict nodulation in soybean, especially by Brandyrhizobium (Sugawara et al., ; Tang et al., ).…”

“…For decades, quantitative trait loci (QTLs) have been used to confirm many agronomically important traits and thereafter have been used to identify desirable traits, which are utilized in gene discovery. QTLs associated with nodulation traits, biological nitrogen fixation and root architecture have been reported in legumes (Bourion et al., ; Diaz et al., ; Gorton, Heath, Pilet‐Nayel, Baranger, & Stinchcombe, ; Heilig, Beaver, Wright, Song, & Kelly, ; Kamfwa, Cichy, & Kelly, ). In early defence responses to nodulation, the signal transduction factors DMI1 , DMI2 and DMI3 were mined via QTLs in Medicago truncatula (Ané et al., ).…”

QTL Mapping of Ineffective Nodulation and Nitrogen Utilization‐Related Traits in the IC‐1 Mutant of Cowpea

“…In soybean, QTL governing nodule number, size, and weight were identified (Tanya et al, 2005; Nicolás et al, 2006; Santos et al, 2013; Hwang et al, 2014), as well as QTL regulating acetylene reduction and plant dry weight (Tanya et al, 2005). Several QTL for nodule number have also been mapped in common bean (Nodari et al, 1993; Tsai et al, 1998; Heilig et al, 2017).…”