Bacterial blight (BB) and fungal blast diseases are the major biotic constraints that limit rice productivity. To sustain yield improvement in rice, it is necessary to developed yield potential of ...the rice varieties by incorporation of biotic stress resistance genes. Tellahamsa is a well-adapted popular high yielding rice variety in Telangana state, India. However, the variety is highly susceptible to BB and blast. In this study, simultaneous stepwise transfer of genes through marker-assisted backcross breeding (MABB) strategy was used to introgress two major BB (Xa21 and xa13) and two major blast resistance genes (Pi54 and Pi1) into Tellahamsa. In each generation (from F.sub.1 to ICF.sub.3) foreground selection was done using gene-specific markers viz., pTA248 (Xa21), xa13prom (xa13), Pi54MAS (Pi54) and RM224 (Pi1). Two independent BC.sub.2 F.sub.1 lines of Tellahamsa/ISM (Cross-I) and Tellahamsa/NLR145 (Cross-II) possessing 92% and 94% recurrent parent genome (RPG) respectively were intercrossed to develop ICF1-ICF.sub.3 generations. These gene pyramided lines were evaluated for key agro-morphological traits, quality, and resistance against blast at three different hotspot locations as well as BB at two locations. Two ICF.sub.3 gene pyramided lines viz., TH-625-159 and TH-625-491 possessing four genes exhibited a high level of resistance to BB and blast. In the future, these improved Tellahamsa lines could be developed as mega varieties for different agro-climatic zones and also as potential donors for different pre-breeding rice research.
Bacterial blight (BB) disease reduces the yield of rice varieties and hybrids considerably in many tropical rice growing countries like India. The present study highlights the development of durable ...BB resistance into the background of an elite maintainer of rice, DRR17B, by incorporating two major dominant genes, Xa21 and Xa33 through marker-assisted backcross breeding (MABB). Through two sets of backcrosses, the two BB resistance genes were transferred separately to DRR17B. In this process, at each stage of backcrossing, foreground selection was carried out for the target resistance genes and for non-fertility restorer alleles concerning the major fertility restorer genes Rf3 and Rf4, using gene-specific PCR-based markers, while background selection was done using a set of 61 and 64 parental polymorphic SSR markers respectively. Backcross derived lines possessing either Xa21 or Xa33 along with maximum genome recovery of DRR17B were identified at BC3F1 generation and selfed to develop BC3F2s. Plants harboring Xa21 or Xa33 in homozygous condition were identified among BC3F2s and were intercrossed with each other to combine both the genes. The intercross F1 plants (ICF1) were selfed and the intercross F2(ICF2) plants possessing both Xa21 and Xa33 in homozygous condition were identified with the help of markers. They were then advanced further by selfing until ICF4 generation. Selected ICF4 lines were evaluated for their resistance against BB with eight virulent isolates and for key agro-morphological traits. Six promising two-gene pyramiding lines of DRR17B with high level of BB resistance and agro-morphological attributes similar or superior to DRR17B with complete maintenance ability have been identified. These lines with elevated level of durable resistance may be handy tool for BB resistance breeding.
Rhizoctonia solani is a polyphagous fungal pathogen that causes diseases in crops. The fungal strains are classified into anastomosis groups (AGs); however, genomic complexity, diversification into ...the AGs and the evolution of pathogenicity-associated genes remain poorly understood.
We report a recent whole-genome duplication and sequential segmental duplications in AG1-IA strains of R. solani. Transposable element (TE) clusters have caused loss of synteny in the duplicated blocks and introduced differential structural alterations in the functional domains of several pathogenicity-associated paralogous gene pairs. We demonstrate that the TE-mediated structural variations in a glycosyl hydrolase domain and a GMC oxidoreductase domain in two paralogous pairs affect the pathogenicity of R. solani. Furthermore, to investigate the association of TEs with the natural selection and evolution of pathogenicity, we sequenced the genomes of forty-two rice field isolates of R. solani AG1-IA. The genomic regions with high population mutation rates and with the lowest nucleotide diversity are enriched with TEs. Genetic diversity analysis predicted the genes that are most likely under diversifying and purifying selections. We present evidence that a smaller variant of a glucosamine phosphate N-acetyltransferase (GNAT) protein, predicted to be under purifying selection, and an LPMP_AA9 domain-containing protein, predicted to be under diversifying selection, are important for the successful pathogenesis of R. solani in rice as well as tomato.
Our study has unravelled whole-genome duplication, TE-mediated neofunctionalization of genes and evolution of pathogenicity traits in R. solani AG1-IA. The pathogenicity-associated genes identified during the study can serve as novel targets for disease control.
Bacterial blight disease of rice caused by
Xanthomonas oryzae
pv.
oryzae
(
Xoo
) is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the ...deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from
Oryza officinalis
possessing broad-spectrum resistance against
Xoo
. In order to understand the inheritance of resistance in the
O. officinalis
accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F
2
population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F
7
generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with
Xoo
and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named
Xa48t
.
In silico
search in the genomic region between the two markers flanking
Xa48t
identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the
Os11g0687900
encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of
Os11g0687900
with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of
Xa48t
.
Background
Rice blast and bacterial leaf blight (BLB) are the most limiting factors for rice production in the world which cause yield losses typically ranging from 20 to 30% and can be as high as ...50% in some areas of Asia especially India under severe infection conditions.
Methods and results
An improved line of Tellahamsa, TH-625-491 having two BLB resistance genes (
xa13
and
Xa21
) and two blast resistance genes (
Pi54
and
Pi1
) with 95% Tellahamsa genome was used in the present study. TH-625-491 was validated for all four target genes and was used for backcrossing with Tellahamsa. Seventeen IBC
1
F
1
plants heterozygous for all four target genes, 19 IBC
1
F
2
plants homozygous for four, three and two gene combinations and 19 IBC
1
F
2:3
plants also homozygous for four, three and two gene combinations were observed. Among seventeen IBC
1
F
1
plants, IBC
1
F
1
-62 plant recorded highest recurrent parent genome (97.5%) covering 75 polymorphic markers. Out of the total of 920 IBC
1
F
2
plants screened, 19 homozygous plants were homozygous for four, three and two target genes along with bacterial blight resistance. Background analysis was done in all 19 homozygous IBC
1
F
2
plants possessing BLB resistance (possessing
xa13
,
Xa21, Pi54
and
Pi1
in different combinations) with five parental polymorphic SSR markers. IBC
1
F
2
-62-515 recovered 98.5% recurrent parent genome. The four, three and two gene pyramided lines of Tellahamsa exhibited varying resistance to blast.
Conclusions
Results show that there might be presence of antagonistic effect between bacterial blight and blast resistance genes since the lines with
Pi54
and
Pi1
combination are showing better resistance than the combinations with both bacterial blight and blast resistance genes.
Background
Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we ...undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (
Pi9
), bacterial leaf blight (BLB) (
Xa4, xa5, xa13, Xa21
), brown planthopper (BPH) (
Bph3, Bph17
), gall midge (GM) (
Gm4, Gm8
) and QTLs for drought tolerance (
qDTY
1.1
and
qDTY
3.1
) through marker-assisted forward breeding (MAFB) approach.
Result
Seven introgression lines (ILs) possessing a combination of seven to ten genes/QTLs for different biotic and abiotic stresses have been developed using marker-assisted selection (MAS) breeding method in the background of Swarna with drought QTLs. These ILs were superior to the respective recurrent parent in agronomic performance and also possess preferred grain quality with intermediate to high amylose content (AC) (23–26%). Out of these, three ILs viz., IL1 (
Pi9
+
Xa4
+
xa5
+
Xa21
+
Bph17
+
Gm8
+
qDTY
1.1
+
qDTY
3.1
), IL6 (
Pi9
+
Xa4
+
xa5
+
Xa21
+
Bph3
+
Bph17
+
Gm4
+
Gm8+ qDTY
1.1
+
qDTY
3.1
) and IL7 (
Pi9+ Xa4
+
xa5
+
Bph3
+
Gm4
+
qDTY
1.1
+
qDTY
3.1
) had shown resistance\tolerance for multiple biotic and abiotic stresses both in the field and glasshouse conditions. Overall, the ILs were high yielding under various stresses and importantly they also performed well in non-stress conditions without any yield penalty.
Conclusion
The current study clearly illustrated the success of MAS in combining tolerance to multiple biotic and abiotic stresses while maintaining higher yield potential and preferred grain quality. Developed ILs with seven to ten genes in the current study showed superiority to recurrent parent Swarna+drought for multiple-biotic stresses (blast, BLB, BPH and GM) together with yield advantages of 1.0 t ha
− 1
under drought condition, without adverse effect on grain quality traits under non-stress.
Broadening of the genetic base for identification and transfer of genes for resistance to insect pests and diseases from wild relatives of rice is an important strategy in resistance breeding ...programs across the world. An accession of Oryza nivara, International Rice Germplasm Collection (IRGC) accession number 105710, was identified to exhibit high level and broad-spectrum resistance to Xanthomonas oryzae pv. oryzae. In order to study the genetics of resistance and to tag and map the resistance gene or genes present in IRGC 105710, it was crossed with the bacterial blight (BB)-susceptible varieties 'TN1' and 'Samba Mahsuri' (SM) and then backcrossed to generate backcross mapping populations. Analysis of these populations and their progeny testing revealed that a single dominant gene controls resistance in IRGC 105710. The BC(1)F(2) population derived from the cross IRGC 105710/TN1//TN1 was screened with a set of 72 polymorphic simple-sequence repeat (SSR) markers distributed across the rice genome and the resistance gene was coarse mapped on chromosome 7 between the SSR markers RM5711 and RM6728 at a genetic distance of 17.0 and 19.3 centimorgans (cM), respectively. After analysis involving 49 SSR markers located between the genomic interval spanned by RM5711 and RM6728, and BC(2)F(2) population consisting of 2,011 individuals derived from the cross IRGC 105710/TN1//TN1, the gene was fine mapped between two SSR markers (RMWR7.1 and RMWR7.6) located at a genetic distance of 0.9 and 1.2 cM, respectively, from the gene and flanking it. The linkage distances were validated in a BC(1)F(2) mapping population derived from the cross IRGC 105710/SM//2 × SM. The BB resistance gene present in the O. nivara accession was identified to be novel based on its unique map location on chromosome 7 and wider spectrum of BB resistance; this gene has been named Xa33. The genomic region between the two closely flanking SSR markers was in silico analyzed for putatively expressed candidate genes. In total, eight genes were identified in the region and a putative gene encoding serinethreonine kinase appears to be a candidate for the Xa33 gene.
Background
Improved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly ...at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL
, Saltol,
associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6–11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the
Saltol
QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29).
Results
Foreground selection was carried out at each generation using five
Saltol-
specific markers and three bacterial blight resistance genes,
Xa21, xa13
and
xa5
. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC
3
F
2
generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC
3
F
4
generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for
Saltol
and
OsSKC1
(
Shoot K
+
Concentration 1
).
Conclusion
DRR Dhan 58, possessing
Saltol
and three bacterial blight resistance genes (
Xa21, xa13
and
xa5
) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.
Aim
To investigate the genetic and pathogenic variability of Xanthomonas oryzae pv. oryzae causing bacterial blight in rice on the remote Andaman Islands, India.
Methods and Results
A total of 27 ...yellow‐pigmented bacterial isolates representing rice fields of Andaman Islands incited blight on the susceptible‐rice cultivar, C14‐8. Phenotypic, pathogenic traits and 16S rRNA gene sequences revealed their identity as X. oryzae pv. oryzae. Virulence profiling indicated the prevalence of seven pathotypes of X. oryzae pv. oryzae on the Islands. Pathotypes‐VI and ‐VII were highly virulent, whereas the pathotype‐I was less virulent. Multilocus sequence typing based on nucleotide sequence polymorphism in nine housekeeping genes dnaK; fyuA; gyrB (two loci): rpoD; fusA; gapA; gltA and lepA clustered 27 isolates into 17 sequence types (STs) segregated into two clonal‐complexes (CC). While CC‐I comprised of isolates from Andaman Island, the CC‐II is a mixture of isolates representing mainland India and Andaman Island. The data revealed trans‐boundary pathogen introduction and a consequent intra‐regional diversification on these islands due to the deployment of different rice cultivars in different regions.
Conclusions
Genotyping and pathotyping of sland isolates revealed seven pathotypes distributed in two clonal complexes with strong indications for trans‐boundary movement and consequent diversification of the bacterial pathogen. Highly virulent pathotypes of X. oryzae pv. oryzae that could overcome combinations of R‐genes, xa13+Xa21 as well as xa5+xa13 were found prevalent in the Andaman Islands
Significance and Impact of the Study
Genetic and virulence analysis of X. oryzae pv. oryzae in the Andaman Islands revealed introduction and host‐mediated regional diversification and local adaptation of X oryzae pv. oryzae. The study calls for the need of multi‐gene pyramiding for durable disease resistance and establishing stringent quarantine measures for safeguarding island agricultural practices in the future.
Bacterial blight (BB) of rice caused by
Xanthomonas oryzae
pv.
oryzae
(
Xoo
), remains a major production constraint in rice cultivation especially in irrigated and rainfed lowland ecosystems in ...India. The pathogen is highly dynamic in nature and knowledge on pathotype composition among the
Xoo
population is imperative for designing a scientific resistance breeding program. In this study, four hundred isolates of
Xoo
collected from diverse rice growing regions of India were analyzed for their virulence and genetic composition. Virulence profiling was carried out on a set of differentials consisting of 22 near isogenic lines (NILs) of IR24 possessing different BB resistance genes and their combinations along with the checks. It was observed that different NILs possessing single BB resistance gene were susceptible to about 59–94% of the
Xoo
isolates except IRBB 13 (containing BB resistance gene
xa13
), which showed susceptibility to about 35% of the isolates. Based on the reaction of the
Xoo
isolates on the differentials, they were categorized into 22 pathotypes. Among the 22 pathotypes, IXoPt-1 and IXoPt-2 were least virulent and IXoPt # 18–22 were highly virulent. Pathotype IXoPt-19 which was virulent on all single BB resistance genes except
xa13
constituted the major pathotype (22.5% isolates) and was widely distributed throughout India (16 states). This was followed by pathotype IXoPt-22 (17.25%) which was virulent on all the NILs possessing single BB resistance genes. Molecular analysis was carried out using two outwardly directed primers complementary to sequence of
IS1112
, a repetitive element of
Xoo
. A high level of genetic polymorphism was detected among these isolates and the isolates were grouped into 12 major clusters. The data indicated complex nature of evolution of the
Xoo
pathotypes and there was no strong correlation between pathotypes and genetic clusters as each genetic cluster was composed of
Xoo
isolates belonging to different pathotypes. The study indicated that none of the single BB resistance genes can provide broad spectrum resistance in India. However, two-gene combinations like
xa5
+
xa13
and different 3 or 4 genes combination like
Xa4
+
xa5
+
xa13, Xa4
+
xa13
+
Xa21
,
xa5
+
xa13
+
Xa21
and
Xa4
+
xa5
+
xa13
+
Xa21
are broadly effective throughout India.
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