Identification Of QTLs For Resistance Research Articles

Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of ‘Pamyati Azieva × Paragon’

Leaf rust (LR) and stem rust (SR) are harmful fungal diseases of bread wheat (Triticum aestivum L.). The purpose of this study was to identify QTLs for resistance to LR and SR that are effective in two wheat-growing regions of Kazakhstan. To accomplish this task, a population of recombinant inbred lines (RILs) of ‘Pamyati Azieva × Paragon’ was grown in the northern and southeastern parts of Kazakhstan, phenotyped for LR/SR severities, and analyzed for key yield components. The study revealed a negative correlation between disease severity and plant productivity in both areas. The mapping population was genotyped using a 20,000 Illumina SNP array. A total of 4595 polymorphic SNP markers were further selected for linkage analysis after filtering based on missing data percentage and segregation distortion. Windows QTL Cartographer was applied to identify QTLs associated with LR and SR resistances in the RIL mapping population studied. Two QTLs for LR resistance and eight for SR resistance were found in the north, and the genetic positions of eight of them have matched the positions of the known Lr and Sr genes, while two QTLs for SR were novel. In the southeast, eight QTLs for LR and one for SR were identified in total. The study is an initial step of the genetic mapping of LR and SR resistance loci of bread wheat in Kazakhstan. Field trials in two areas of the country and the genotyping of the selected mapping population have allowed identification of key QTLs that will be effective in regional breeding projects for better bread wheat productivity.

Resistant carrots to Alternaria dauci or tasty carrots: should we choose?

The carrot ideotype for carrot breeders could be a variety resistant to Alternaria leaf blight-the main foliar disease on carrot worldwide-with a low level of bitterness as consumers consider it as an undesirable taste of carrots. Our previous investigation on carrot resistance to Alternaria dauci allowed the identification of resistance QTLs (rQTLs). Based on these results, breeding for a higher level of resistance is possible but we could interrogate about the impact of selecting these genomic regions on carrot bitterness. To answer this question, we combined chemical and sensorial analyses of a set of resistant and susceptible carrot genotypes evaluated in different environments to identify the metabolites involved in bitterness. The genetic control and heritability field experimentation and colocalizations between rQTLs and metabolite QTLs (mQTLs) were searched in order to evaluate the link between bitterness and resistance traits. Our results showed that selecting the genomic regions mainly involved in carrot resistance is possible without compromising carrot taste. However, the colocalization of rQTLs and mQTLs suggest that some genomic regions are involved in the expression of both traits and should be avoided or even counter selected. INTRODUCTION While breeding for varieties highly resistant to Alternaria dauci is a top priority for carrot seed companies, consumers are more and more demanding on gustative quality, especially low bitter carrots. Amon others, terpens and polyacetylenes are considered key compounds for bitterness in carrots (Simon et al. 1980; Seljasen et al. 2001). Relying on sensory and chemical analyses, Kreutzmann et al. (2008) highlighted that a small number of metabolites, among them eight terpens, could predict bitterness. However, while the genetic control of carrot resistance to A. dauci has already been investigated, leading to the identification of rQTLs (Quantitative Trait Loci involved in resistance) in different genetic backgrounds (Le Clerc et al., 2009; 2015), no information were available except very recently published by Keilwagen at al. (2017) on terpens and polyacetylenes. Identifying the genomic regions involved in resistance and/or bitterness will be very helpful for breeders to develop resistant varieties while avoiding increasing bitterness. To answer this question, chemical and sensory analyses were performed on a set of five carrot genotypes during three years, in four environments to identify the terpens involved in bitterness. These metabolites were characterized during two consecutive years in field trials in a population already segregating for resistance to Alternaria dauci and their genetic control was determined. The colocalization between previously identified rQTLS and mQTLS (QTLs involved in the accumulation of metabolites) were examined and recommendations were made for breeders.

Construction of high-density linkage map and identification of QTLs for resistance to sorghum downy mildew in maize (Zea mays L.)

Sorghum downy mildew (SDM), caused by obligate biotrophic fungi Peronosclerospora sorghi, is an economically important disease of maize. The genetics of resistance was reported to be polygenic thereby necessitating identification of QTLs for resistance to SDM to initiate effective marker-assisted selection programs. During post-rainy and winter season of 2012, 645 F2:3 progeny families from the cross CML153 (susceptible) × CML226 (resistant) were screened for their reaction to SDM. Characterization of QTLs affecting resistance to SDM was undertaken using the genetic linkage map with 319 polymorphic SSR and SNP marker loci and the phenotypic data of F2:3 families. Three QTLs conferring resistance to SDM were consistently identified on chromosomes 2, 3 and 6 in both seasons. The resistant parent CML226 contributed all the QTL alleles conferring resistance to SDM. The major QTL located on chromosome 2 explained 38.68% of total phenotypic variation in the combined analysis with a LOD score of 9.12. All the three QTL showed partially dominant gene effects in combined analysis. The detection of more than one QTL supports the hypothesis that quantitative genes control resistance to P. sorghi. The generation was advanced to F6 using markers linked to major QTLs on chromosomes 2 and 3 to derive 33 SDM resistant maize inbred lines.

Genetic analysis and identification of QTLs for resistance to cucumber mosaic virus in chili pepper (Capsicum annuum L.)

A pepper (Capsicum annuum) inbred line ‘BJ0747-1-3-1-1’ was found to exhibit resistance to a cucumber mosaic virus (CMV) local isolate (CMV-HB). In order to exploit the genetic mechanism of CMV resistance in this pepper line, inheritance and genetic linkages of CMV resistance were studied. The CMV-resistant ‘BJ0747-1-3-1-1’ (P1) was crossed to the susceptible line ‘XJ0630-2-1-2-1-1’ (P2), and the F2 and back-cross populations (B1 and B2) were generated for segregation analysis following a mixed inheritance model. Analysis of the segregation data revealed that CMV resistance in ‘BJ0747-1-3-1-1’ is controlled by two partially additive-dominant major genes and additive-dominant polygenes. Analysis of the results from two growth seasons also identified two stable and major QTLs for CMV resistance that collectively explained 55 % of the trait variation. One of the two major QTLs was found on linkage group 8 (LG8) between markers TS52 and HpmsE1-43, and accounted for 37.7–43.5 % of the variation in the two inoculation experiments. The other QTL on LG4 between markers UBC843 and S74 was found to be responsible for 10.7–11.2 % of the trait variation. QTLs with minor effects on CMV resistance were also identified. This work provides an example for genetic analysis and QTL mapping of other disease-resistance genes in pepper and the findings should be useful for molecular marker-assisted breeding programs that aim at developing disease-resistant cultivars in peppers.

Development of Introgression Lines and Identification of QTLs for Resistance to Sheath Blight

In this study,two random BC2F2 populations were developed by cross and backcross,in which two major hybrid restorer lines Shuhui 527 and Minghui 86 were used as recurrent parents respectively,and Jiangxisimiao used as donor.The bulks of the BC2F2 populations were inoculated with Rhizoctonia solani to screen the lines resistant to sheath blight,and 49 resistant introgression lines(ILs) were selected.The genotypes of ILs were analyzed with evenly distributed polymorphic SSR markers,and a total of 12 significant loci were identified by χ2 test analysis.Among them,two allelic frequency-deviation loci were located in the same or near regions identified in the previous studies.In the field test without artificial inoculation,there was no significant difference between all the agronomic traits investigated in the selected ILs and their recurrent parents.Under heavily diseased conditions,six ILs with Shuhui 527 background and two ILs with Minghui 86 background showed similar agronomic traits and significantly higher resistance to sheath blight than their recurrent parents at two experimental sites,which can be served as immediate sources of sheath blight resistance for hybrid rice breeding and directly used in hybrid rice production.

Identification of QTLs for resistance to anthracnose to two Colletotrichum species in pepper

Pepper (Capsicum spp.) anthracnose caused by Colletotrichum spp. is a serious disease damaging pepper production in Asian monsoon regions. For QTL mapping analyses of anthracnose resistance, an introgression BC1F2 population was made by interspecific crosses between Capsicum annuum ‘SP26’ (susceptible recurrent parent) and Capsicum baccatum ‘PBC81’ (resistant donor). Both green and red fruits were inoculated with C. acutatum ‘KSCa-1’ and C. capsici ‘ThSCc-1’ isolates and the disease reactions were evaluated by disease incidence, true lesion diameter, and overall lesion diameter. On the whole, distribution of anthracnose resistance was skewed toward the resistant parent. It might indicate that one or two major QTLs are present. The introgression map consisting of 13 linkage groups with a total of 218 markers (197 AFLP and 21 SSR), covering a total length of 325 cM was constructed. Composite interval mapping analysis revealed four QTLs for resistance to ‘KSCa-1’ and three QTLs for ‘ThSCc-1’ isolate, respectively. Interestingly, the major QTLs (CaR12.2 and CcR9) for resistance to C. acutatum and C. capsici, respectively, were differently positioned but there were close links between the minor QTL CcR12.2 for C. capsici and major QTL CaR12.2 as well as the minor QTL CaR9 for C. acutatum and major QTL CcR9. These results will be helpful for marker-assisted selection and pyramiding two different anthracnose-resistant genes in commercial pepper breeding.