Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.)

Abstract

BackgroundXanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BB), an emerging disease in rice in West-Africa which can induce up to 50 % of yield losses. So far, no specific resistance gene or QTL to African Xoo were mapped. The objectives of this study were to identify and map novels and specific resistance QTLs to African Xoo strains.ResultsThe reference recombinant inbred lines (RIL) mapping population derived from the cross between IR64 and Azucena was used to investigate Xoo resistance. Resistance to African and Philippine Xoo strains representing different races was assessed on the RIL population under greenhouse conditions. Five major quantitative trait loci (QTL) for resistance against African Xoo were located on different chromosomes. Loci on chromosomes 1, 7, 9, 10 and 11 explained as much as 13 %, 37 %, 13 %, 11 % and 15 % of resistance variation, respectively. A major novel QTL located on chromosome 7 explained 37 % of the phenotypic variance to the African Xoo corresponding to race A3 whereas that on chromosome 11 is effective to all African races tested. Together with genes and QTLs for resistance to bacterial blight previously described, the QTLs described here were mapped onto the reference O. sativa subs japonica (var. Nipponbare) physical map.ConclusionWe characterized new resistance QTLs. While some co-localize with known resistance genes/QTLs to Asian strains, others are specific to African strains. We result with new information on genes and QTLs for resistance to bacterial blight that will be useful for controlling the disease.

Allelic variation for broad‐spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population

“…Overlapping genetic regions associated with disease resistance for both X. oryzae pathovars were mapped on chromosomes 4 for Xoc BAI5, MAI3 and Xoo BAI3, and on 11 for Xoc MAI3, and Xoo BAI3, at 30–32 Mbp and 27–29 Mbp, respectively (Table S6). The region on chromosome 4 colocalizes with a recently detected locus Xo1 that is effective against multiple Xoc and Xoo strains (Triplett et al ., ), and the region on chromosome 11 was reported to contain resistance for Xoo but not for Xoc (Djedatin et al ., ).…”

“…qXO-2-1, qXO-2-2, qXO-5-1, qXO-5-3 and qXO-12-1), these regions were not shown previously to confer resistance to African X. oryzae strains. We used a larger and more diverse set of strains, including different Xoo races, and demonstrated a broader effectiveness for the previously identified loci qXO-4-1, qBB-7-1, qXO-10-1 and qXO-11-2 (Djedatin et al, 2016;Triplett et al, 2016). Two QTL, qXO-4-1 and qXO-11-2, coincide with clusters of R genes previously identified for Asian Xoo resistance on chromosome 4 (Xa1, Xa2, Xa12, Xa14, Xa31 and Xa38) and chromosome 11 (Xa3/26, Xa4, Xa10, Xa21, Xa22 and Xa23) (Kim et al, 2015).…”

“…Understanding the resistance and susceptibility mechanisms to X. oryzae in rice Despite advances in understanding how Asian X. oryzae elicit resistance or susceptibility in the host, the knowledge of resistance and susceptibility mechanisms to African X. oryzae is limited (Djedatin et al, 2016;Triplett et al, 2016). Both Xoc and Xoo contain and use TAL effectors for virulence, but their TAL repertoires are distinct (Cernadas et al, 2014).…”

“…Djedatin et al . recently mapped disease resistance QTL effective against African Xoo strains, located on rice chromosomes 1, 7, 9, 10 and 11 (Djedatin et al ., ). Interestingly, the QTL on chromosome 11 confers resistance to both Asian and African Xoo .…”

“…Over 40 R genes against Asian Xoo strains have been mapped (Hutin et al, 2015;Kim et al, 2015); however, most of these R genes are not effective in controlling the distinct strains of Xoc and Xoo present in sub-Saharan Africa (Gonzalez et al, 2007). Djedatin et al recently mapped disease resistance QTL effective against African Xoo strains, located on rice chromosomes 1, 7, 9, 10 and 11 (Djedatin et al, 2016). Interestingly, the QTL on chromosome 11 confers resistance to both Asian and African Xoo.…”