Characterization of gall midge

resistance in rice genotypes using gene

specific markers

Girish K. S.
Ph. D. Scholar
Department of Agril. Entomology
College of Agriculture, Raichur
The Asian rice gall midge (ARGM) Orseolia
oryzae (Wood-Mason)

First reported as an unidentified pest of rice

in Bihar, India, by Riley (1881).

A significant portion of yield loss due to

damage in several rice-growing countries
including India, China, Thailand, Sri Lanka,
Myanmar, Indonesia, Bangladesh, and
Vietnam.

Conservative economic estimate of yield

losses from gall midge is about US$ 500
million in Asia and US$ 80 million in India
alone.

Rated as third most important pest of rice.

 Rice – Gall midge interactions
Kakatiya the first gall midge (GM)resistant variety released in 1975.

Since then, > 100 rice varieties resistant to gall midge have been released for
cultivation.

Systematic evaluation of over 25,000 accessions of rice germplasm has led to

identification of more than 500 sources of resistance to gall midge and majority
of these are landraces from northeastern states of India.

Differential reaction of same genotype against gall midge populations at different

rice-growing areas reflected intraspecific variations and helped in the detection
of its geographically distinct populations (biotypes).

Roy et al. (1969) first suspected the occurrence of gall midge biotypes (GMB).

At present seven biotypes – GMB 1 to GMB 6 and GMB4M

11 gall midge resistant genes – Gm1 through Gm 11

 Rice – Gall midge interactions
Gene-for-gene relation

• Each of the biotypes showed a specific range of virulence against

R genes.

• Each R gene conferred resistance to specific biotypes

• None of the R genes conferred resistance to all biotypes and

none of the biotypes showed virulence against all the R genes.
 Phenotype screening

Set Genotypes screened Phenotypic reaction

Set 1 17 Nil damage
Set 2 31 Marginal damage ≤20
Set 3 18 20 – 50 % damage
Set 4 6 > 50% damage
Set 5 22 Susceptible
TOTAL 97

Dutta et al. 2014

Table 1: Nature and effectiveness of gall midge resistance genes in rice against
different biotypes
Chr. HR Reaction to gall midge biotypes
Group Source Gene
no. type GMB1 GMB2 GMB3 GMB4 GMB5 GMB6 GMB4M
I W1263 Gm1 9 – HR R S R S R R S

II Phalguna Gm2 4 +HR R R S S R S S

II ARC5984 Gm5 ? +HR R R R S R S S

II Dukong 1 Gm6 4 +HR R R R S R S S

II RP2333-156- Gm7 4 +HR R R R S R S S

8
II Madhuri-L9 Gm9 7 +HR R R R S R S S

II BG308 Gm10 ? +HR R R R S R S S

III CR57- Gm11 12 +HR R R R R S S S

MR1523
IV RP2068 Gm3 4 +HR R R R R S S R

IV Abhaya Gm4 8 +HR R R R R S S R

IV Jhitpiti/ Gm8 8 – HR R R R R S S R
Aganni
V TN1 none - S S S S S S S

HR: Hyper sensitive reaction Makkar and Bentur, 2017

Tagging, Mapping and Cloning Gall Midge Resistance Gene
To date PCR-based linked molecular markers have been developed
for 8 of the 11 genes
resistance genes
Gm2, gm3, Gm6, Gm7 noted as a cluster on chromosome 4.
Gm4 and Gm8 are located on chromosome 8
Gm1 located on chromosome 9
Gm12 located on chromosome 11

Yasala et al. 2012

Three of the genes viz., gm3, Gm4, and Gm8, have been cloned
through map-based approach, and candidate genes for these have
been identified as
gm3: NB-ARC (LOC_Os04g52970.1) (Sama et al. 2014),
Gm4: NBS-LRR (LOC_Os08g09670.1) (Divya et al. 2015)
Gm8: Proline rice protein (Dutta et al. 2014).
Table 2: Details of designed primers for fine-mapping of gm3 and validation of the
candidate gene NB-ARC gene

Sama et al. 2014

 Table 3: Marker-trait co-segregation pattern with four polymorphic
SSR markers and the gene-specific gm3del3 marker in F10 RILs of the
cross Tn1 X rP2068-18-3-5

a Heterozygous lines were not tested with SSR marker

b R-RP2068 allele; H-allele of both parents; S-TN1 allele3 Sama et al. 2014
Fig. 1 Genotyping of 16 BC2F2 plants from the cross of B95-1/RP2068-18-3-
5//B95-1*2 with gm3del3 marker

Sama et al. 2014

Fig. 2 Fine-mapping of gm3 candidate gene NB-ARC with designed (gm3SSr4) and known
SSR markers (rM17468, rM17473 and rM17480) on rice chromosome 4.

Figures on left indicate physical position in mega base pair (Mb) and on right indicate
genetic distance in cM
Sama et al. 2014
Table 4: Details of gene specific markers used in characterizing rice genotypes.

Dutta et al. 2014

Fig. 3: Amplification pattern with gm3del3, LRR-del, Proline rich protein (PRP) functional
markers in rice genotypes for presence of Gm3, Gm4 and Gm8 genes

Dutta et al. 2014

Gm1 is mapped within 0.18 Mb region on chromosome 9 between
the SSR markers RM23941 and RM23956 (Sundaram, 2007).

Gm2 within 0.66 Mb region on chromosome 4 between the SSR

markers RM17473 and RM17503 (Sundaram, 2007).

Gm3 within 0.56 Mb region on chromosome 4 between the SSR

markers RM17480 and RMgm3SSR4 (Sama et al., 2010).

Gm4 within 0.33 Mb region on chromosome 8 between the SSR

markers RM22551 and RM22562 (Himabindu, 2009).

Gm5 is tagged using RAPD markers OPR-19, OPP-09, OPB-14, OPQ-05

and OPE-01 but not yetmapped (Katiyar et al., 2000).

Gm6 within 0.59 Mb region on chromosome 4 between the RFLP

markers RG476 and RG214 (Katiyar et al., 2001).
Gm7 towards downstream on chromosome 4 using AFLP marker
SA598 (Sardesai et al., 2002).

Gm8 within 0.43 Mb region on chromosome 8 between the SSR

markers RM22685 and RM22709 (Sama, 2011)

Gm11 within 1.7 Mb region on chromosome 12 between the SSR

markers RM28574 and RM28706 (Himabindu et al., 2010).
 Table 5: Details of the genes from different gall midge resistance regions

Total size of the Total no. of

R gene Chr. Location Chr. Region
region (bp) genes
Gm1 9 7656946 - 8156946 500000 62
Gm2,3,6,7 4 31023295 – 31848200 824905 162
Gm4 8 5370894 – 5870894 500000 98
Gm8 8 8769772 – 9269772 500000 83
Gm11 12 24258416 – 25959620 1701204 248
Total 4026109 690

Dutta et al. 2014

 Chr 4 Chr 8 Chr 9 Chr 12

Fig. 4: Linkage maps of gall midge resistance genes on different chromosomes

Makkar and Bentur, 2017

 Pyramiding of Gall Midge-Resistant Genes in Rice
Gene pyramiding offers an excellent approach to incorporate wide
range and durable resistance against gall midge in rice.

Better insights into the genetics of resistance, R (resistant) gene

mapping, allelic relationships, and linkage are necessary for
pyramiding of resistant genes.

The best combination of genes suggested is Gm4 + Gm8 or

Gm3 + Gm8
 Conclusions
• Rice-gall midge interactions may be in a state of evolutionary flux.

• Ingenious adaptation of the insect against this first line of defense

has rendered the plant more prone and secure host for the gall
former.

• No single approach would provide lasting resistance to the gall

midge.

• Novel approaches need to be continuously explored to stay one

step ahead of this evolutionary miracle pest.