Improvement of Upland Rice Variety by Pyramiding Drought Tolerance QTL with Two Major Blast Resistance Genes for Sustainable Rice Production

Vishalakshi BalijaUmakanth Bangale Senguttuvel PonnuvelKalyani Makarand Barbadikar Srinivas Prasad MadamshettySanjeeva Rao DurbhaHari YadlaSheshu Madhav Maganti

Research Paper

Improvement of Upland Rice Variety by Pyramiding Drought Tolerance QTL with Two Major Blast Resistance Genes for Sustainable Rice Production

Vishalakshi Balija1,6,#, Umakanth Bangale1,#, Senguttuvel Ponnuvel2, Kalyani Makarand Barbadikar1, Srinivas Prasad Madamshetty3, Sanjeeva Rao Durbha4, Hari Yadla5, Sheshu Madhav Maganti1

(Biotechnology Division, ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad 500030, India; Hybrid Rice Division, ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad 500030, India; Plant Pathology Division, ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad 500030, India; Plant Physiology Division, ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad 500030, India; Regional Agricultural Research Station, Professor Jayashankar Telangana State Agricultural University, Warangal 506006, India; Department of Biotechnology, Acharya Nagarjuna University, Guntur 522510, India; These authors contributed equally to this work)

Varalu is an early maturing rice variety widely grown in the rainfed ecosystem preferred for its grain type and cooking quality. However, the yield of Varalu is substantially low since it is being affected by reproductive drought stress along with the blast disease. The genetic improvement of Varalu was done by introgressing a major yield QTL,qDTY, along with two major blast resistance genes i.e.andthrough marker-assisted backcross breeding. Both traits were transferred till BC2generation and intercrossing was followed to pyramid the two traits. Stringent foreground selection was carried out using linked markers as well as peak markers (RM28099, RM28130, RM511 and RM28163) for the targeted QTL (qDTY), RM206 forand RM224 forExtensive background selection was done using genome-wide SSR markers. Six best lines (MSM-36, MSM-49, MSM-53, MSM-57, MSM-60 and MSM-63) havingqDTYand two blast resistance genes in homozygous condition with recurrent parent genome of 95.0%?96.5% having minimal linkage drag of about 0.1 to 0.7 Mb were identified. These lines showed yield advantage under drought stress as well as irrigated conditions. MSM-36 showed better performance in the national coordinated trials conducted across India, which indicated that improved lines of Varalu expected to replace Varalu and may have an important role in sustaining rice production. The present study demonstrated the successful marker-assisted pyramiding strategy for introgression of genes/QTLs conferring biotic stress resistance and yield under abiotic stress in rice.

blast resistance; drought stress; marker-assisted gene pyramiding; rainfed ecosystem; upland rice

Rice (L.) is a primary source of nutrition for more than half of the world’s population. Despite the saturation in genetic yield, demand for rice is increasing with the ever increasing population. Rice is also cultivated in around 23 million hectares of rainfed ecosystem where yields are significantly affected due to frequent occurrence of drought (Serraj et al, 2011), and blast (Dean et al, 2012), and global climate changecan further increase the drought stress (Wassmann et al,2009). Also, yield is affected due to drought spells in irrigated conditions (Bernier et al, 2009a).

Among many QTLs identified for drought stress tolerance,qDTYoffers significant yield potential under reproductive-stage drought stress by contributing 51% genetic variance (Bernier et al, 2007). Blast disease caused by(anamorph) is another production constraint commonly observed in the rainfed ecosystem (Dean et al, 2012). So far, above 100 genes have been reported to aid in blast resistance (Devi et al, 2020). Among them, two significant blast resistance genesandconfer broad-spectrum resistance against predominant races of the pathogen in India (Mackill and Bonman, 1992; Sharma et al, 2005). Marker-assisted gene pyramiding (MAGP) is a precise, rapid and efficient method to pyramid desired genes/QTLs along with maximum recovery of recurrent parent genome within two to three backcrosses (Jamaloddin et al, 2020).

Varalu is a popular variety cultivated in major upland areas of India. It is affected by reproductive drought stress and blast disease. Hence, this study aimed to genetic improvement of Varalu by introgressing a major yield QTL (qDTY) along with two major blast resistance genes (and) through MAGP.

Results

Introgression of qDTY12.1 into Varalu

Through foreground selection, 13 F1plants from Cross-I [Varalu × Vandana near-isogenic line (NIL)], 40 BC1F1, 25 BC2F1and 26BC2F2plants were found positive forqDTY(Fig. 1). Polymorphic assay between Varalu and Vandana NIL identified 200 SSR markers, which were uniformly spread across the rice genome. Two best BC1F1plants possessing the maximum recurrent parent genome recovery (RPGR, 76.0%) andqDTYwere backcrossed to produce BC2F1, and two best BC2F1plants were used to produce BC2F2population (= 422). Finally, five BC2F2plants displaying homozygousqDTYgenomic region and high grain yield under reproductive drought stress portraying 82.0%?85.0% of RPGR were identified. The recombinant selection was performed among five BC2F2plants to minimize the linkage drag atqDTYlocus and found the recombination breakpoints (RBP) ranged from 3.6 to 4.3Mb at the proximal and distal ends, respectively (Fig. S1-A). Among them, one plant (VVN-117-34-26) with the maximum RPGR of nearly 85.0% was used for intercrossing.

Fig. 1. Schematic representation of marker-assisted gene pyramiding followed for introgression ofqDTYfor improvement of grain yield under reproductive stage drought stress and blast resistance genes (and) in Varalu variety.

NIL, Near-isogenic line; BPT-LT, Elite rice line with the genetic background of Samba Mahsuri containing two blast resistance genesand; RPGR, Recurrent parent genome recovery; IC, Intercross.

Introgression of blast resistance genes into Varalu

Ten F1plants derived from Cross-II [Varalu × BPT-LT (an elite rice line with the genetic background of Samba Mahsuri containing two blast resistance genesand)], 25 BC1F1, 20 BC2F1and 34 BC2F2plants were found positive for bothand(Fig. 1). A total of 180 markers showed polymorphism betweenVaralu and BPT-LT were used for background analysis. Three best BC1F1plants possessing a maximum RPGR of 77.0% were used to generate BC2F1plants and two best BC2F1plants were used to produce BC2F2plants. Finally, six BC2F2plants showed a high resistant level to blast with 86.0%?90.0% of RPGR. The RBP of six plants atlocus was observed at 2.1 to 0.5 Mb of donor genome segment at proximal and distal ends, respectively (Fig. S1-B).In case oflocus, all the six plants showed RBP of 2.1 Mb at the proximal end, and ranged from 0.6 to 1.6 Mb at the distal end. Two BC2F2plants (VLT-175-13-10 and VLT-183-98-31) havingandin homozygous conditionwith the maximum RPGR of nearly 90.0% were forwarded for intercrossing (IC).

Fig. 2. Graphical representation of selected pyramided lines of Varalu for donor genome introgression associated with blast resistance genesandon chromosome 11 andqDTYon chromosome 12.

A, Atlocus, a donor segment introgression was limited to only about 0.3 Mb at the proximal end; atlocus, about 0.2 Mb donor genome was observed at the proximal end.

B, AtqDTYlocus, a donor genomic region about 0.7 and 0.1 Mb at the proximal and distal ends, respectively, was observed in four lines on chromosome 12. Two lines (MSM-36 and MSM-60) showed limited donor segments in comparison with other lines.

NIL, Near-isogenic line; BPT-LT, Elite rice line with the genetic background of Samba Mahsuri containing two blast resistance genesand.

Pyramiding of qDTY12.1 and blast resistance genes into Varalu

The best homozygous BC2F2plants obtained from the two crosses were intercrossed for pyramiding the target genes/QTL (qDTY,and). The best three ICF1plants having all the three genes were selfed to generate ICF2population. Among these, 20 ICF2plants were homozygous for all the three genes (qDTY,and). Six best pyramided lines (MSM-36, MSM-49, MSM-53, MSM-57, MSM-60 and MSM-63) were identified based on blast resistance and grain yield under reproductive stage drought stress (Fig. 1). Background analysis with 120 polymorphic SSR markers revealed 95.0%?96.5% of RPGR (Fig. S1-C). The recombinant selection among the six best lines revealed a segment of 0.3 and 0.2 Mb of donor genome segment at the distal and proximal ends ofandloci, respectively (Fig. 2-A). Moreover, at qDTYlocus, 0.7 and 0.1 Mb of donor genome segment was found at the proximal and distal ends, respectively (Fig. 2-B). Among the best six lines, MSM-36 and MSM-60 showed very less linkage drag in the three loci compared to the other four entries.

Performance of improved lines for yield under drought and irrigated conditions

Among the 422 BC2F2individuals of Cross-I, 26 homozygous plants containingqDTYwith higher yields ranging from 14.8 to 23.4 g/plant, which was chosen for intercrossing. Twenty of the 800 ICF2s displayed higher grain yield per plant (14.96 to 18.74 g) than the recurrent parent (RP) (11.6 g) under reproductive stage drought stress (Table 1). Most of theintercrossed lines had higher plant height except MSM-49, which was shorter than Varalu (Table 1 and Fig. S2-A). Interestingly, the measured yield contributing traits were also superior to RP in these lines (Table 1 and Fig. S2-B). However, there was little difference in the flag leaf length and days to 50% flowering among the improved lines (Table 1). Among these, six improved lines (MSM-36, MSM-49, MSM-53, MSM-57, MSM-60 and MSM-63) having superior yield characteristics and similar grain type like RP in reproductive stage drought stress conditions were selected and further assessed for yield under irrigated conditions (Table 1; Fig. S2-B and-C).

Under irrigated conditions, three lines, MSM-36, MSM-49 and MSM-60, exhibited higher grain yield (22.84, 22.40 and 22.13 g, respectively) than the recurrent parent (20.72 g) (Table 1).

Evaluation of disease reaction in improved lines of Varalu

The six BC2F2plants of Cross-II and 20 homozygous pyramided lines ICF2to ICF5noted ‘0’ (Fig. S3) and ‘0?2’ blast scores, respectively (Table 1 and Fig. 3), indicating high level of blast resistance.

Moreover, MSM-36 out yielded its RP in Zone VII ofAll India Coordinated Rice Improvement Programme(AICRIP, consisting of five states, Telangana, Andhra Pradesh, Karnataka, Tamil Nadu and Kerala) with yield advantage of 18.8% and 13.8% under drought and controlled conditions, respectively. The average blast disease susceptibility index of MSM-36 at multiple locations was 2.95 compared to Varalu of 6.20 (Table S2).

Grain quality analysis of improved lines

In addition to the brown hull colour, long slender grain type and cooking quality parameters of the six pyramided lines were assessed and found MSM-36 and MSM-60 were particularly similar to RP (Table 2).

Discussion

Several drought-tolerant QTLs detected from diverse sources (Kumar et al, 2007; Vikram et al, 2011) are less exploited in breeding programmes. There is a keen interest in selecting the progenies having higher yield even under the stress, which is offered by a few QTLs likeqDTY(Bernier et al, 2009b). The effectiveness ofqDTYwas evident from the introgressions of Vandana and Sabitri under drought and irrigated conditions (Mishra et al, 2013; Kumar et al, 2014). Severe incidence of blast disease was also seen in the upland ecosystem (Asibi et al, 2019), which can be addressed by pyramiding major blast resistance genes.

Fig. 3. Phenotypic screening of pyramided lines (Pi54 + Pi1 + qDTY) against blast disease.

A, All the intercross derived lines and donor parent BPT-LT (an elite rice line with the genetic background of Samba Mahsuri containing two blast resistance genesand)were highly resistant whereas the recurrent parent Varalu showed susceptible against blast.

B, Lesions were observed on the leaf surface of the recurrent parent Varalu while the pyramided lines and donor parent showed no lesion on the leaf surface.

Table 2. Grain and cooking quality of selected pyramided lines of Varalu.

HRR, Head rice recovery; GL, Grain length; GW, Grain width; GL/GW, Ratio of grain length to width; VOC, Very occasionally; ASV, Alkali spreading value; AC, Amylose content; GC, Gel consistency; LS, Long slender; MB, Medium bold.

Marker-assisted breeding strategy has been employed to improve rice varieties for resistance against biotic and biotic stresses independently (Dixit et al, 2020). But few reports exist on the development of combined resistant versions to biotic and abiotic stress resistant varieties (Dixit et al, 2014, 2020; Muthu et al, 2020).

RPGRs of the two backcrosses (Cross-I and Cross-II) and intercross were 82.0%?85.0%, 86.0%?90.0% and 95.0%?96.5%, respectively, which were higher than the reported introgression studies (Khan et al, 2018; Chukwu et al, 2019; Swathi et al, 2019). Moreover, the improved lines displayed very close recombination breakpoints at both ends of the three loci, indicating less donor genome introgression. Anyaohaet al (2019) improved the rainfed rice variety FUNAABOR-2 for grain yield under drought stress by introgressingqDTYandqDTYusing marker-assisted selection with the minimum linkage drag of about 0.8 Mb.Likeandpyramided Tellahamsa lines (Jamaloddin et al, 2020), individuals of backcross population having both the genes noted higher resistance score of 0 than the individuals with only(0?2) or(2?3). Thus,might provide broad spectrum resistance than(Patroti et al, 2019). The NILs possessing two genes or single gene can be used as donors for the deployment in the rice improvement programme. Like Sabitri linesunder lowland reproductive stage drought stress (Mishra et al, 2013), the backcross population having properly delimitedqDTYregion of Dixit et al (2012) showed higher grain yield than the lines possessing either one.

Due to proper phenotypic selection, the mean grain yields of pyramided lines under drought (16.53 g) and irrigated (20.71 g) conditions were higher than the RP (11.60 g and 20.72 g) (Table 1).The results indicated that agro-morphological and cooking quality characters of the improved lines of Varalu were similar to RP except MSM-49 with shorter plant height and lower alkali spreading value. Under the reproductive stage drought stress and irrigated conditions, MSM-36 and MSM-60 were identified as the best lines with high grain yield and desirable cooking quality (Table 2), and MSM-36 noted superior performance in the Zone VII of AICRIP trial.

The present study combined a major drought QTL (qDTY) and two major blast resistance genes (and) into the genetic background of upland rice variety Varalu. Two best improved Varalu lines, MSM-36 and MSM-60 possessing high yield under drought stress and blast resistance along with > 96% RPGR are expected to replace Varalu. These lines did not show any yield penalty under irrigated condition and can be disseminated for cultivation in drought- prone niches of India.

methods

Rice materials

The long slender and early maturing (90?95 d) elite rice variety, Varalu (WGL-20471 × CR-544-1-2), was used as the recurrent parent. Vandana NIL and BPT-LT were used as donors for drought (qDTY) (Bernier et al, 2007) and blast (two resistance genesand), respectively. Two independent crosses. Varalu × Vandana NIL (Cross-I) and Varalu × BPT-LT (Cross-II) were made followed by selection of positive lines and backcrossing with Varalu up to BC2F2and intercrossing at BC2F2for pyramiding both traits. The selected lines possessingqDTY +were advanced through the pedigree method from ICF3to ICF5for field evaluation of agronomical traits against blast and reproductive stage drought stress (Fig. 1).

DNA extraction and genotyping

Genomic DNA was isolated from 21-day-old seedlings of the parents, F1, backcross and intercross generations (Murray and Thompson, 1980). Devi et al (2015) procedure was used for PCR amplification. The foreground selection ofqDTYwas done using peak marker as well as linked markers RM511, RM28099 (forqDTY), RM28130 and RM28163 (forqDTY), while RM206 for, RM224 for(Dixit et al, 2012; Patroti et al, 2019) (Table S1). A set of 635 SSR markers covering every 2?5 Mb interval were selected (http://rice. plantbiology.msu.edu/) for background selection. The identified polymorphic markers between the donors and the recurrent parent were utilized for background selection in backcross and intercross populations. The assessment of RPGR was done based on the SSR marker data using the Graphical Genotypes (GGTs) V2.0 software.

Screening of derived lines under reproductive stage drought stress

Backcross and intercross derived populations were screened for reproductive stage drought stress (Venuprasad et al, 2007) at the research farm, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India, in a random block design with 20 cm × 20 cm row spacing. Agro-morphological traits like plant height, number of tillers per plant, number of panicles per plant, flag leaf length, days to 50% flowering, 1000-grain weight and grain yield were measured.

Screening for blast

The blast screening of all the backcross and intercross lines of Varalu was done in a uniform blast nursery at ICAR-IIRR (Umakanth et al, 2017) using Standard Evaluation System with 0?9 scales (IRRI, 2002).

Screening of improved lines under irrigated conditions

Twenty-five-day-old seedlings of selected lines along with the parents were transplanted in the lowland irrigated plot in a random block design with 150 cm × 20 cm row spacing. Irrigation was given twice a week and all the agro- morphological traits measured in drought plot were also recorded. Further, two best lines (MSM-36 and MSM-60) were also screened across 10 different AICRIP locations under reproductive stage drought stress and irrigated conditions (http://www.icar-iirr.org/aicrip.htm).

Quality analysis

The harvested seeds of the selected lines in triplicate and their parents were shade dried up to 12%?14% moisture content. Intact milled grains were used to determine grain type by length to width ratio (IRRI, 2004) and alkali spreading value (Juliano et al, 1990). Milled grains ground to 100 mesh powders were analyzed for gel consistency (Cagampang, 1973) and amylose content (Juliano, 1971).

Statistical analysis

The Duncan’s multiple range test was carried out to compare significant difference of improved lines with recurrent parent for agro-morphological traits using XLSTAT (Version 2020.5).The coefficient of variation, standard deviation and standard error of the mean were calculated by using the MS Excel package to determine the significant variation between the lines.

AcknowledgEment

The authors acknowledge the Department of Biotechnology, New Delhi, India for providing funds for carrying out the research work.

Supplemental DATA

The following materials are available in the online version of this article at http://www.sciencedirect.com/journal/rice-science; http://www.ricescience.org.

Fig. S1. Graphical representation of BC2F2selected lines.

Fig. S2. Phenotypes of improved lines.

Fig. S3. Blast phenotypic screening of BC2F2selected lines of Cross-II (Varalu × BPT-LT) and their parents.

Table S1. Details of SSR markers used for foreground selection.

Table S2. Performance of best pyramided lines under drought and controlled conditions in national trials (Zone VII).

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14 August 2020;

8 January 2021

Sheshu Madhav Maganti (sheshu24@gmail.com; sheshu_24@yahoo.com)

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