White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature). A meta-QTL analysis of the 37 QTL was conducted using the genetic linkage map of Stampede x Red Hawk population as the reference. The 37 QTL condensed into 17 named loci (12 previously named and five new) of which nine were defined as meta-QTL WM1.1, WM2.2, WM3.1, WM5.4, WM6.2, WM7.1, WM7.4, WM7.5, and WM8.3. The nine meta-QTL had confidence intervals ranging from 0.65 to 9.41 Mb. Candidate genes shown to express under S. sclerotiorum infection in other studies, including cell wall receptor kinase, COI1, ethylene responsive transcription factor, peroxidase, and MYB transcription factor, were found within the confidence interval for five of the meta-QTL. The nine meta-QTL are recommended as potential targets for MAS for partial resistance to white mold in common bean.

BackgroundAluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.ResultsFive genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al3+ specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1.ConclusionsHigh ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-153) contains supplementary material, which is available to authorized users.

Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).

ABSTRACT. The interaction between polygalacturonase-inhibiting proteins (PGIPs), produced by plants, and endopolygalacturonases (PGs), produced by fungi, limits the destructive potential of PGs and can trigger plant defense responses. This study aimed to i) investigate variation in the expression of different common bean (Phaseolus vulgaris L.) genotypes and its relationship with resistance to white mold (Sclerotinia sclerotiorum); ii) determine the expression levels of PvPGIP genes at different time points after inoculation with white mold; and iii) investigate differences in PvPGIP gene expression between two white mold isolates with different levels of aggressiveness. Four bean lines were analyzed, including two lines from a recurrent selection for white mold (50/5 and 84/6), one resistant line that was not adapted to Brazilian conditions (Cornell 605), and one susceptible line (Corujinha). Gene expression was investigated at 0, 1, 2, 3, and 5 days after inoculation. The isolate UFLA 03 caused no significant difference in the relative expression of any gene examined, and was inefficient in discriminating among the genotypes. For the isolate UFLA 116, all of the genes were differentially expressed, as they were associated with resistance to white mold, and the expressions increased until the third day after inoculation. The 50/5 line was not significantly different from the Corujinha line for all of the genes analyzed. However, this line had a resistance level that was similar to that of Cornell 605, according to the straw test. Therefore, the incorporation of PvPGIP genes can increase the resistance of lines derived from recurrent selection.

The development of aluminum (Al)-tolerant cultivars is a complementary strategy to overcome the constraints caused by Al toxicity on acid soils and can contribute positively to the food supply for the growing global population. A major Al tolerance quantitative trait locus in maize is controlled by a citrate transporter encoded by ZmMATE1. Our goal was to evaluate the impact of the superior allele of ZmMATE1 on the yield performance of maize lines and hybrids cultivated on acid soils. Near-isogenic lines carrying the superior allele of ZmMATE1, and the recurrent Al-sensitive parent were crossed with elite lines, generating near-isogenic hybrids contrasting for these alleles. All maize genotypes carrying this superior allele were more Al tolerant in nutrient solution than their isogenic counterparts having the ZmMATE1 allele derived from the Al-sensitive parent. These genotypes were cultivated in control and Al stress soils for 2 yr. Aluminum toxicity caused a significant yield reduction of 18.7% for lines and 14.7% for hybrids over the 2 yr. The yield performance of maize genotypes declined in the second year compared with the first year, probably due to water deficiency after the grain-filling stage. The superior allele of ZmMATE1 in maize hybrids conferred yield gains from 21 to 48% compared with the hybrids harboring the alternative allele in the Al stress soil in the first and second years, respectively. As this superior allele is rare in maize and is likely absent in several elite germplasms, molecular breeding based on ZmMATE1 can improve maize yield stability on acid soils.