Delineating meta-quantitative trait loci for anthracnose resistance in common bean (Phaseolus vulgaris L.)

Abstract

Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the devastating disease affecting common bean production and productivity worldwide. Several quantitative trait loci (QTLs) for anthracnose resistance have been identified. In order to make use of these QTLs in common bean breeding programs, a detailed meta-QTL (MQTL) analysis has been conducted. For the MQTL analysis, 92 QTLs related to anthracnose disease reported in 18 different earlier studies involving 16 mapping populations were compiled and projected on to the consensus map. This meta-analysis led to the identification of 11 MQTLs (each involving QTLs from at least two different studies) on 06 bean chromosomes and 10 QTL hotspots each involving multiple QTLs from an individual study on 07 chromosomes. The confidence interval (CI) of the identified MQTLs was found 3.51 times lower than the CI of initial QTLs. Marker-trait associations (MTAs) reported in published genome-wide association studies (GWAS) were used to validate nine of the 11 identified MQTLs, with MQTL4.1 overlapping with as many as 40 MTAs. Functional annotation of the 11 MQTL regions revealed 1,251 genes including several R genes (such as those encoding for NBS-LRR domain-containing proteins, protein kinases, etc.) and other defense related genes. The MQTLs, QTL hotspots and the potential candidate genes identified during the present study will prove useful in common bean marker-assisted breeding programs and in basic studies involving fine mapping and cloning of genomic regions associated with anthracnose resistance in common beans.

Genome-wide meta-QTL analyses provide novel insight into disease resistance repertoires in common bean

“…MQTL analysis can detect stable QTLs regardless of their genetic background, chronology and location in the corresponding original investigation [ 16 , 26 , 30 , 96 ]. In comparison to the MQTLs reported in the previous study on white mold [ 13 ] and anthracnose [ 20 ], we identified one further overlapping MQTL named MQTL7P.1 located on chromosome 7 conveying resistance against white mold disease. Four MQTLs (MQTL1P.1, MQTL5P.1, MQTL7P.1, MQTL8P.1) in our study overlapped with five MQTLs of anthracnose disease [ 20 ], three of which located at the closest region to previous study.…”

“…In comparison to the MQTLs reported in the previous study on white mold [ 13 ] and anthracnose [ 20 ], we identified one further overlapping MQTL named MQTL7P.1 located on chromosome 7 conveying resistance against white mold disease. Four MQTLs (MQTL1P.1, MQTL5P.1, MQTL7P.1, MQTL8P.1) in our study overlapped with five MQTLs of anthracnose disease [ 20 ], three of which located at the closest region to previous study. Furthermore, four MQTLs including MQTL2P.1, MQTL5P.1, MQTL8P.1, MQTL9P.1 located at the same regions with the hotspot of QTLs in previous study on anthracnose [ 20 ].…”

“…Out of 152 QTLs from 44 QTL populations, 57 QTLs were successfully projected on two common bean reference maps. Although MQTL analyses on common bean has already been conducted on the amount of iron and zinc content [ 95 ], resistance to anthracnose [ 20 ], and white mold [ 13 ], to the best of our knowledge, this is the first comprehensive multiple disease resistance meta-QTLs (MDR-MQTLs) analysis to decipher disease resistance-associated repertories in the crop.…”

“…However, individual QTLs reported in the literature are associated with particular genotypes and environmental conditions and in the cases of diseases; they depend on the genotype of the pathogen in different experiments [ 16 , 17 , 18 , 19 ]. It is necessary to identify and investigate cultivars containing resistance genes conferring resistance against multiple races of pathogens [ 20 ].…”

“…Meta-analysis of QTLs is applied to compilation of data from independent mapping populations [27,28]. This approach has been used to find MQTL for crop disease resistance including Fusarium head blight in wheat [29], Phytophthora-related diseases in cocoa [30], cyst nematode in soybean [31], white mold [13] and anthracnose [20] in common bean. Furthermore, there are several studies describing multiple disease resistance meta-QTLs (MDR-MQTLs) conveying resistance against different types of pathogens in different crops [32,33,34,35,36].…”