Both BC1 and F2 populations have been developed for the TuMV-resistant B.
juncea lines TWBJ14 and TWBJ20. For line TWBJ14, a number of plants in both BC1 and F2 populations were phenotyped and the resistance/susceptibility
segregation ratio closely fitted a Mendelian model based on the action of two recessive genes (1:3 and 1:15 respectively). For line TWBJ20, only the BC1
population was phenotyped due to time limitations. However, the resistance/susceptibility segregation ratio of this population was not significantly different from a Mendelian model based on the action of two recessive genes (1:3). The complementation test performed suggested that at least one resistance gene was not shared between these two lines. There were three phenotypes (0, + and +N) in
TWBJ14 BC1 and F2 populations, in comparison to the two phenotypes (0 and +N)
in TWBJ20 BC1 population. This also suggested there were different resistance
genes involved in these two resistant lines.
Two BC1 segregating populations were used for genetic mapping because of their
higher mapping efficiency than F2 populations. Due to the limitation of research
funding for a PhD project, it was not possible to genotype all the 427 individual plants in the two BC1 populations. Therefore, subsets of selected plants have been
genotyped using the Illumina® Infinium SNP Array. This might bring down the mapping efficiency to a certain degree. However, based on the genotypic data obtained, it appears both genetic linkage analysis and QTL mapping have been properly implemented. In both genetic maps, decent numbers of markers were spread across the chromosomes, with 14-34 non-overlapping markers on each chromosome.
The QTL analysis suggested that it was an additive two-QTL model involved in the TuMV resistances in both resistant B. juncea lines. One highly significant QTL and one less significant QTL contributed to the resistance independently with an additive effect. In both BC1 populations, the QTL mapping results were consistent
with the two recessive gene model suggested by the phenotypic distributions. Plant recessive resistance occurs when mutation arises in specific host proteins (targets of pathogen effector) encoded by susceptibility genes (S-genes) (Eckardt, 2002; Pavan
et al. 2010). Recessive resistance is more prevalent for plant viruses than for other plant pathogens (Kang et al., 2005). There have been several reports about pathogen resistances controlled by two recessive genes in plants. Ruffel et al. (2006) reported that complementation of two recessive resistance genes, pvr2 and pvr6, were necessary for the resistance to Pepper veinal mottle virus (PVMV) in Capsicum
(PVMV and TuMV both belong to the Potyvirus genus). Vallejos et al. (2010) identified two recessive resistance genes bs5 and bs6 in Capsicum with resistance to
Xanthomonas euvesicatoria that causes bacterial spot disease. The combined effect of these two genes gave full resistance to all races of bacterial spot in peppers. Iyer and McCouch (2004; 2007) detected and cloned two recessive genes (xa5 and xa13) controlling resistance to different strains of Xanthomonas oryzae pv. oryzae and suggested a new model for the function of recessive resistance in plant-bacterial interactions. As for resistances to insects, Hou et al. (2011) detected two recessive genes to the brown planthopper in rice using QTL analysis. Two QTL named
bph22(t) and bph23(t) had LOD scores of 2.92 and 3.15 and explained 11.3% and 14.9% of phenotypic variation, respectively.
As mentioned in section 1.4.4, more than half of the reported Potyvirus resistance genes are recessive, which are believed to be based on a passive mechanism. There have been numerous reports on natural recessive virus resistance genes associated with translation initiation factors (eIF4E / eIF(iso)4E and eIF4G / eIF(iso)4G) in Arabidopsis, brassicas, lettuce, pepper, bean, rice, as well as many others (Le Gall et al., 2011). In Brassica rapa, several TuMV resistance genes related to the absence of susceptibility factors eIF4E / eIF(iso)4E have been reported, such as retro01, ConTR01 (Rusholme et al., 2007) and retro02 (Qian et al., 2013).
studies, three copies of eIF4E and three copies of eIF(iso)4E have been identified and sequenced in a genomic library of the TuMV-susceptible B. rapa line R-o-18 (Jenner et al., 2010) and a genomic library of TuMV-resistant B. rapa line RLR22 (Nellist et al., 2014). Based on the conserved domains and motifs found in eIF4E and eIF4G using hmmpfam, Qian et al. (2013) identified all the eIF4 genes in the B. rapa genome (eIF4E and eIF(iso)4E share certain similar protein domains and motifs, as do eIF4G and eIF(iso)4G). A total of 11 eIF4E / eIF(iso)4E and 14 eIF4G / eIF(iso)4G gene candidates were identified across B. rapa genome (Qian et al. 2013). Additionally, I have searched any other annotations of eIF4 genes in different online databases. With this information, the positions of these candidate genes were compared to the regions of the QTL that I identified for the TuMV resistances in B. juncea lines TWBJ14 and TWBJ20 (Fig. 4.13 and Fig. 4.14).
Figure 4.13 − Linkage groups A06 and A02 of Brassica juncea TWBJ14 BC1 population showing QTL involved in Turnip mosaic virus resistance and
linked markers.
QTL are indicated on left hand side. The red vertical bar and the rectangle represent confidence interval and peak LOD scores. The numbers on the left hand side of the linkage group represent genetic distance in cM at named markers shown to the right.
Figure 4.14 − Linkage groups A06 and A08 of Brassica juncea TWBJ20 BC1
population showing QTL involved in Turnip mosaic virus resistance and linked markers.
QTL are indicated on left hand side. The red vertical bar and the rectangle represent confidence interval and peak LOD scores. The numbers on the left hand side of the linkage group represent genetic distance in cM at named markers shown to the right.
After comparisons of candidate locations with QTL confidence intervals, one predicted eIF4G candidate gene (Bra038615) on A06 lies in the confidence interval (12.3 cM) of the QTL on A06 in line TWBJ14, according to the physical position. What is more, Bra038615 is not far from the TuMV resistance QTL on A06 in line TWBJ20, with the physical distance being approximately 3,829,000-7,802,000 bp. Additionally, the confidence interval of the QTL on A06 in line TWBJ14 includes the TuMV resistance QTL on A06 in TWBJ20, according to the physical position. This implies that Bra038615 could be the candidate gene for the resistance QTL on A06 in both lines.
In addition, another two eIF4G-like genes Bra008429 and Bra020407 (Qian et al., 2013) lie in the confidence interval (30.1 cM) of the TuMV resistance QTL on A02 in line TWBJ14. The candidate genes BraA.eIF4E.c (Bra021026),