Search

Characterization of physiological traits affected by rice breeding for grain yield under drought conditions shows that atmospheric and soil stresses strengthen the relationship between leaf traits and yield across extensive trials in South Asia., Direct selection for yield under drought has resulted in the release of a number of drought-tolerant rice varieties across Asia. In this study, we characterized the physiological traits that have been affected by this strategy in breeding trials across sites in Bangladesh, India, and Nepal. Drought- breeding lines and drought-tolerant varieties showed consistently longer flag leaves and lower stomatal density than our drought-susceptible check variety, IR64. The influence of environmental parameters other than drought treatments on leaf traits was evidenced by close grouping of treatments within a site. Flag-leaf length and width appeared to be regulated by different environmental parameters. In separate trials in the Philippines, the same breeding lines studied in South Asia showed that canopy temperature under drought and harvest index across treatments were most correlated with grain yield. Both atmospheric and soil stress strengthened the relationships between leaf traits and yield. The stable expression of leaf traits among genotypes and the identification of the environmental conditions in which they contribute to yield, as well as the observation that some breeding lines showed longer time to flowering and higher canopy temperature than IR64, suggest that selection for additional physiological traits may result in further improvements of this breeding pool.

Among the different challenges related to rice (Oryza sativa L.) cultivation, drought, bacterial leaf blight (BLB), and blast are the key stresses that significantly affect grain yield (GY) in rice. To ameliorate this issue, marker-assisted forward breeding (MAFB) coupled with a simultaneous crossing approach was used to combine three drought tolerant quantitative trait loci (QTL)-qDTY1.1 , qDTY3.1 , and qDTY12.1 -four BLB genes-Xa4, xa5, xa13, and Xa21-and one blast-resistance gene, Pi9, in the elite rice cultivar Lalat. The introgression lines (ILs) developed in the current study were phenotypically screened for drought, BLB, and blast resistance at the F7 -F8 generation. Under the reproductive stage (RS) drought stress, the yield advantage of ILs, with major-effect QTL (qDTY) over elite parent Lalat, ranges from 9 to 124% in DS2019 and from 7 to 175% in WS2019. The selected ILs were highly resistant to BLB, with lesion lengths ranging from 1.3 to 3.0 cm and blast scores ranging from 1 to 3. ILs that were tolerant to RS drought, resistant to BLB, and blast disease and had similar or higher yields than Lalat were analyzed for grain quality. Six ILs were found to have similar grain quality characteristics to Lalat including hulling, milling, head rice recovery (HRR), chalkiness, alkali spreading value (ASV), and amylose content (AC). This study showed that MAFB, together with simultaneous crossing, would be an effective strategy to rapidly combine multiple stresses in rice. The ILs developed in this study could help to ensure yield sustainability in rainfed environments or be used as genetic material in future breeding programs.

Highlights • Genetic gain for rice grain yield for International Rice Research Institute drought breeding program was estimated. • Positive trend of 0.68 %, 0.87 %, 1.9 % under irrigated control, moderate and severe drought achieved. • Superiority of new rice varieties over currently grown demonstrated on farmers’ fields. • International Rice Research Institute developed rice varieties can protect farmers from crop losses under drought conditions., The complexity of genotype × environment interactions under drought reduces heritability, which determines the effectiveness of selection for drought tolerance and development of drought tolerant varieties. Genetic progress measured through changes in yield performance over time is important in determining the efficiency of breeding programmes in which test cultivars are replaced each year on the assumption that the new cultivars will surpass the older cultivars. The goal of our study was to determine the annual rate of genetic gain for rice grain yield in a drought-prone rainfed system in a series of multi-environment trials conducted from 2005 to 2014 under the Drought Breeding Network of Indian sites in collaboration with the International Rice Research Institute (IRRI). Our results show a positive trend in grain yield with an annual genetic yield increase of about 0.68 % under irrigated control, 0.87 % under moderate reproductive stage drought stress and 1.9 % under severe reproductive stage drought stress due to breeding efforts. The study also demonstrates the effectiveness of direct selection for grain yield under both irrigated control as well as managed drought stress screening to improve yield in typical rainfed systems. IRRI's drought breeding programme has exhibited a significant positive trend in genetic gain for grain yield over the years under both drought stress as well as favorable irrigated control conditions. Several drought tolerant varieties released from the programme have outperformed the currently grown varieties under varied conditions in the rainfed environments on farmers’ fields.

Occurrence of multiple abiotic stresses in a single crop season has become more frequent than before. Most of the traditional donors possessing tolerance to abiotic stresses are tall, low-yielding with poor grain quality. To facilitate efficient use of complex polygenic traits in rice molecular breeding research, we undertook development of introgression lines in background of high-yielding, semi-dwarf varieties with good grain quality. The study reports the development and evaluations of over 25,000 introgression lines in eleven elite rice genetic backgrounds for improvement of yield under multiple abiotic-stresses such as drought, flood, high/low temperature. The developed introgression lines within each genetic background are near isogenic/recombinant inbred lines to their recipient recurrent parent with 50 to 98% background recovery and additionally carry QTLs/genes for abiotic stresses. The multiple-stress tolerant pyramided breeding lines combining high yield under normal situation and good yield under moderate to severe reproductive-stage drought, semi-dwarf plant type with good grain quality traits have been developed. The introgression lines in dwarf backgrounds open new opportunity to improve other varieties without any linkage drag as well as facilitate cloning of QTLs, identification and functional characterization of candidate genes, mechanisms associated with targeted QTLs and the genetic networks underlying complex polygenic traits.

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 (qDTY1.1 and qDTY3.1) 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+ qDTY1.1+ qDTY3.1), IL6 (Pi9+ Xa4+ xa5+ Xa21+ Bph3+ Bph17+ Gm4+ Gm8+ qDTY1.1+ qDTY3.1) and IL7 (Pi9+ Xa4+ xa5+ Bph3+ Gm4+ qDTY1.1+ qDTY3.1) 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.

Background Traditional rice (Oryza sativa) varieties are valuable resources for the improvement of drought resistance. qDTY 3.2 is a drought-yield quantitative trait locus that was identified in a population derived from the traditional variety Moroberekan and the drought-susceptible variety Swarna. In this study, our aim was to characterize the physiological mechanisms associated with qDTY 3.2 . Our approach was to phenotype fifteen BC2F3:4 lines for shoot and root drought resistance-related traits as compared to Swarna in the field under well-watered and drought stress conditions. Four BC2F3:4 lines contrasting for yield under drought were selected for detailed characterization of shoot morphology, water use related traits, flowering time and root system architecture in the field as well as in controlled environments (lysimeters in a greenhouse, and gel imaging platform in a growth chamber). Results Across five field experiments, grain yield correlated significantly with root growth along the soil profile, flowering time, and canopy temperature under drought conditions. The four selected BC2F3:4 lines showed earlier flowering time, reduced distribution of root growth to shallow soil layers which resulted in lower water uptake (between 0 and 30 cm) and drought-induced increased distribution of root growth to deep soil layers (between 30 and 60 cm) as compared to Swarna in the field. Root system architecture phenotypes were confirmed in whole root systems in lysimeters, and corresponded to higher numbers of root tips in a gel imaging platform, highlighting the potential stability of some root traits across different growth stages and systems. Conclusions We conclude that earlier flowering time, reduced shallow root growth, and drought-induced increased deep root growth are associated with the presence of qDTY 3.2 since these phenotypes were consistently observed in the selected QTL lines with full introgression of qDTY 3.2 . We hypothesize that the qDTY 3.2 associated RSA phenotypes led to better use of water and metabolic resources which, combined with earlier flowering time, improved yield under drought.

The elite Indian rice variety, Naveen is highly susceptible to major biotic and abiotic stresses such as blast, bacterial blight (BB), gall midge (GM) and drought which limit its productivity in rainfed areas. In the present study, a combined approach of marker-assisted forward (MAFB) and back cross (MABC) breeding was followed to introgress three major genes, viz., Pi9 for blast, Xa21 for bacterial blight (BB), and Gm8 for gall midge (GM) and three major QTLs, viz., qDTY1.1, qDTY2.2 and qDTY4.1 conferring increased yield under drought in the background of Naveen. At each stage of advancement, gene-based/linked markers were used for the foreground selection of biotic and abiotic stress tolerant genes/QTLs. Intensive phenotype-based selections were performed in the field for identification of lines with high level of resistance against blast, BB, GM and drought tolerance without yield penalty under non-stress situation. A set of 8 MAFB lines and 12 MABC lines with 3 to 6 genes/QTLs and possessing resistance/tolerance against biotic stresses and reproductive stage drought stress with better yield performance compared to Naveen were developed. Lines developed through combined MAFB and MABC performed better than lines developed only through MAFB. This study exemplifies the utility of the combined approach of marker-assisted forward and backcrosses breeding for targeted improvement of multiple biotic and abiotic stress resistance in the background of popular mega varieties.

Additional File 1: Table S1. Gene based/linked markers used for foreground selection for blast, BLB, BPH, GM and drought resistance/tolerance genes/QTLs and their validation in the developed lines Table S2. List of parents, markers used for parental polymorphism and foreground selection in introgression lines of Swarna+drought Table S3. Allele size of different gene based/linked markers linked to different trait of interest.

Additional File 2: Figure S1. Screening of the ILs for BLB, blast and gall midge. (a) screening for bacterial leaf blight resistance (b) screening for blast resistance (c) Screening for BPH reaction of ILs under glass house condition (d) BPH screening of ILs under hotspot location.

Photosynthates generated after heading contributes to 60% - 80% of grain yield in rice. Delay in leaf senescence can contribute to a long grain-filling period and thereby increased yield. The objective of this study was to identify genomic region(s) responsible for delayed leaf senescence (DLS) and validate the role of underlying candidate genes in controlling target traits. 302 BC2F4 backcross-derived lines (BILs) developed from a cross between Swarna and Moroberekan were phenotyped for two seasons (DS2016 and WS2017) for chlorophyll content and yield parameters. KASPar-SNP assays based genotyping data with 193 SNPs of mapping population was used to identify the targeted genomic region(s). Significant positive correlation was observed between the two most important determinants of DLS traits viz., RDCF (reduced decline degree of chlorophyll content of flag leaf) and RDCS (reduced decline degree of chlorophyll content of second leaf) with plant height (PH), grain number per panicle (GPN), panicle length (PL), number of tiller (NT) and grain yield (GY). A total of 41 and 29 QTLs with phenotypic variance (PVE) ranging from 8.2 to 25.1% were detected for six DLS traits during DS2016 and WS2017, respectively. Out of these identified QTLs, 19 were considered as stable QTLs detected across seasons. 17 of the identified stable QTLs were found to be novel. In-silico analysis revealed five key genes regulating chlorophyll metabolism. Expression analysis of these genes confirmed their strong association with the senescence pattern in leaf tissue of parents as well as selected phenotypically extreme lines. The identified stable QTLs regulating DLS traits and validation of potential candidate genes provides insight into genetic basis of delayed senescence and is expected to contribute in enhancing grain yield through genomics-assisted breeding (GAB).

The investigation conducted with 25 rice genotypes comprising both Basmati and non-basmati types revealed significant differences among the genotypes for the yield, its components and some grain quality characteristics. The magnitude of differences between PCV and GCV was relatively low for all the traits, indicating less environmental influence. The GCV was higher for the characters alkali spread value, yield per plant and effective panicles. High heritability coupled with high genetic advance as per cent of mean was recorded for days to 50% flowering, plant height, panicle length, effective panicles per plant, spikelets per panicle, filled grains per panicle, test weight, yield per plant, brown rice length, brown rice L/B ratio, kernel length, kernel L/B ratio, kernel length after cooking, elongation ratio and alkali spread value indicating the additive gene effects in the genetic control of these traits and can be improved by simple selection in the present breeding material.

Reducing water requirements and lowering environmental footprints require attention to minimize risks to food security. The present study was conducted with the aim to identify appropriate root traits enhancing rice grain yield under alternate wetting and drying conditions (AWD) and identify stable, high-yielding genotypes better suited to the AWD across variable ecosystems. Advanced breeding lines, popular rice varieties and drought-tolerant lines were evaluated in a series of 23 experiments conducted in the Philippines, India, Bangladesh, Nepal and Cambodia in 2015 and 2016. A large variation in grain yield under AWD conditions enabled the selection of high-yielding and stable genotypes across locations, seasons and years. Water savings of 5.7–23.4% were achieved without significant yield penalty across different ecosystems. The mean grain yield of genotypes across locations ranged from 3.5 to 5.6 t/ha and the mean environment grain yields ranged from 3.7 (Cambodia) to 6.6 (India) t/ha. The best-fitting Finlay-Wilkinson regression model identified eight stable genotypes with mean grain yield of more than 5.0 t/ha across locations. Multidimensional preference analysis represented the strong association of root traits (nodal root number, root dry weight at 22 and 30 days after transplanting) with grain yield. The genotype IR14L253 outperformed in terms of root traits and high mean grain yield across seasons and six locations. The 1.0 t/ha yield advantage of IR14L253 over the popular cultivar IR64 under AWD shall encourage farmers to cultivate IR14L253 and also adopt AWD. The results suggest an important role of root architectural traits in term of more number of nodal roots and root dry weight at 10–20 cm depth on 22–30 days after transplanting (DAT) in providing yield stability and preventing yield reduction under AWD compared to continuous flooded conditions. Genotypes possessing increased number of nodal roots provided higher yield over IR64 as well as no yield reduction under AWD compared to flooded irrigation. The identification of appropriate root architecture traits at specific depth and specific growth stage shall help breeding programs develop better rice varieties for AWD conditions.

Dry direct-seeded rice (DSR) is an alternative crop establishment method with less water and labor requirement through mechanization. It provides better opportunities for a second crop during the cropping season and therefore, a feasible alternative system to transplanted lowland rice. However, lodging is one of the major constraints in attaining high yield in DSR. Identification of QTLs for lodging resistance and their subsequent use in improving varieties under DSR will be an efficient breeding strategy to address the problem. In order to map the QTLs associated with lodging resistance, a set of 253 BC3F4 lines derived from a backcross between Swarna and Moroberekan were evaluated in two consecutive years. A total of 12 QTLs associated with lodging resistance traits [culm length (qCL), culm diameter (qCD), and culm strength (qCS)] were mapped on chromosomes 1, 2, 6, and 7 using 193 polymorphic SNP markers. Two major and consistent effect QTLs, namely qCD1.1 (with R2 of 10%) and qCS1.1 (with R2 of 14%) on chromosome 1 with id1003559 being the peak SNP marker (flanking markers; id1001973-id1006772) were identified as a common genomic region associated with important lodging resistance traits. In silico analysis revealed the presence of Gibberellic Acid 3 beta-hydroxylase along with 34 other putative candidate genes in the marker interval region of id1001973-id1006772. The positive alleles for culm length, culm diameter, and culm strength were contributed by the upland adaptive parent Moroberekan. Our results identified significant positive correlation between lodging related traits (culm length diameter and strength) and grain yield under DSR, indicating the role of lodging resistant traits in grain yield improvement under DSR. Deployment of the identified alleles influencing the culm strength and culm diameter in marker assisted introgression program may facilitate the lodging resistance under DSR.

To improve the grain yield of the lowland-adapted popular rice variety Samba Mahsuri under reproductive-stage drought (RS) and to understand the interactions between drought QTLs, two mapping populations were developed using marker-assisted selection (MAS) and marker-assisted recurrent selection (MARS). The mean grain yield of pyramided lines (PLs) with qDTY 2.2 + qDTY 4.1 in MAS is significantly higher under RS and irrigated control than lines with single QTLs. Among MARS PLs, lines with four qDTYs (qDTY 1.1 + qDTY 2.1 + qDTY 3.1 + qDTY 11.1 ) and two QTLs (qDTY 1.1 + qDTY 11.1 ) yielded higher than PLs with other qDTY combinations. The selected PLs showed a yield advantage of 0.3–2.0 t ha−1 under RS. An allelic profile of MAS PLs having same qDTY combination but with different yields under drought was studied. Hierarchical clustering grouped together the selected lines with high yield under drought. Epistasis test showed the interaction of qDTY 4.1 and qDTY 9.1 loci with qDTY 7.1 significantly increased yield under drought and all the lines with higher yield under drought possessed the conserved region of qDTY 7.1 on chromosome 7. The positive interactions among QTLs, effectiveness of QTLs in different backgrounds, introgression of DTY QTLs together with resistance to biotic stresses shall help enhance grain yield under RS.