QTLs for tolerance of drought and breeding for tolerance of abiotic and biotic stress: an integrated approach

Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach

The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.

Pyramiding of qDTY1.1 and qDTY3.1 into rice mega-variety Samba Mahsuri-Sub1: physiological performance under water deficit conditions

Water deficit is a crucial factor causing huge loss to rice productivity. The present study aimed to develop a multiple stress tolerant genotype by pyramiding drought tolerant yield QTLs qDTY1.1 and qDTY3.1 into high yielding rice variety Samba Mahsuri Sub-1(SMS) through marker assisted pyramiding. To achieve this six introgression lines of SMS carrying qDTY1.1 (SAB) were crossed with DRR-50, an Essentially Derived Variety of SMS carrying qDTY3.1. The SAB lines are taller than SMS due to tight linkage between qDTY1.1 and wild type SD-1. Therefore, F2 generation of crosses were screened for recombinants between SD-1 and qDTY1.1. Phenotyping of 1530 F2 plants representing three F2 populations from 35 F1 hybrids, identified 305 dwarf plants. Three dwarf F2 plants along with three others carrying qDTY1.1 and qDTY3.1 were forwarded to F3 generation. From the six F3 (SABD) lines fourteen pyramided progenies were selected and forward to F4 generation. The six SABD F3 lines SABD-7, SABD-8, SABD-9, SABD-76, SABD-79 and SABD-80 along with parents were evaluated under moisture stress (MS) for various physiological parameters. Chlorophyll and relative water content were more, while canopy temperature and malonaldehyde (MDA) content were lesser in SABD lines compared to parents indicating tolerance under MS. Variance due to genotypes was highly significant for all the yield related traits except test weight. Based on seed morphology, agronomic characters and physiological parameters six superior lines SABD-9-3, SABD-9-2, SABD-9-6, SABD-9-7, SABD-76-2 and SABD-76-6 performing better under MS were identified, which could be released after multi-location evaluation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01387-5.

Genome-wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance

Drought stress is a serious threat to rice productivity. Investigating genetic variations between drought-tolerant (DT) and drought-sensitive (DS) rice cultivars may decipher the candidate genes/regulatory regions involved in drought stress tolerance/response. In this study, whole-genome resequencing data of four DS and five DT rice cultivars were analyzed. We identified a total of approximately 4.8 million single nucleotide polymorphisms (SNPs) and 0.54 million insertions/deletions (InDels). The genetic variations (162,638 SNPs and 17,217 InDels) differentiating DS and DT rice cultivars were found to be unevenly distributed throughout the rice genome; however, they were more frequent near the transcription start and stop sites than in the genic regions. The cis-regulatory motifs representing the binding sites of stress-related transcription factors (MYB, HB, bZIP, ERF, ARR, and AREB) harboring the SNPs/InDels in the promoter regions of a few differentially expressed genes (DEGs) were identified. Importantly, many of these DEGs were located within the drought-associated quantitative trait loci. Overall, this study provides a valuable large-scale genotyping resource and facilitates the discovery of candidate genes associated with drought stress tolerance in rice.

Capturing Genetic Variability and Identification of Promising Drought-Tolerant Lines in Exotic Landrace Derived Population Under Reproductive Drought Stress in Rice

Drought is one of the most predominant abiotic stresses in this century, leading to a drastic reduction in the yield of rainfed rice ecosystems. Breeding of drought-resilient rice varieties is very much in demand for sustainable rice production in drought-prone rainfed ecology. An experiment was designed under irrigated non-stress and drought-stress situations involving an exotic drought-tolerant landrace (Chao Khaw) and a high-yielding aromatic rice cultivar (Kasturi), and an F_2:4 derived population of 156 breeding lines was developed at IRRI South Asia Hub, Hyderabad. The objective of the study was to assess the genetic variability, drought tolerance behavior, and identify promising breeding lines for different rice ecologies and drought breeding programs. Restricted maximum likelihood (REML) analysis using the mixed model approach revealed a considerable genetic variation in the population for yield and yield contributing traits in non-stress and drought-stress conditions. We observed very high heritability for all the selected traits under stress 2015 WS (73.8% to 85.3%) and 2016 WS (72.4% to 93.5%) and non-stress 2015 WS (68.2% To 92.9%) and 2016 WS (61.4% to 92.6%) environments, indicating possible selection for grain yield under drought stress and non-stress with the same precision level. None of the secondary traits except harvest index and biomass included in our study showed a positive association with grain yield, indicating indirect selection's ineffectiveness in improving yield under drought. A total of 48 promising breeding lines were found to have a better yield than donor Chao Khaw (up to 38% advantage) and popular drought-tolerant cultivars Shabhagidhan (up to 48% advantage) in stress conditions and recommended for rainfed upland ecology, 34 breeding lines under the well-watered condition suited for rainfed lowland ecology. Overall, the study found 21 common breeding lines that showed their superiority in non-stress and under drought stress situations, fitting best in rainfed lowland ecology with occasional drought occurrence. The large genetic variation found in this population can be exploited further to develop a few forward breeding high-yielding lines with better drought tolerance ability and used as drought donors in drought breeding programs.

Breeding rice for a changing climate by improving adaptations to water saving technologies

Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.

Integrated Strategies for Durable Rice Blast Resistance in Sub-Saharan Africa

Rice is a key food security crop in Africa. The importance of rice has led to increasing country-specific, regional, and multinational efforts to develop germplasm and policy initiatives to boost production for a more food-secure continent. Currently, this critically important cereal crop is predominantly cultivated by small-scale farmers under suboptimal conditions in most parts of sub-Saharan Africa (SSA). Rice blast disease, caused by the fungus Magnaporthe oryzae, represents one of the major biotic constraints to rice production under small-scale farming systems of Africa, and developing durable disease resistance is therefore of critical importance. In this review, we provide an overview of the major advances by a multinational collaborative research effort to enhance sustainable rice production across SSA and how it is affected by advances in regional policy. As part of the multinational effort, we highlight the importance of joint international partnerships in tackling multiple crop production constraints through integrated research and outreach programs. More specifically, we highlight recent progress in establishing international networks for rice blast disease surveillance, farmer engagement, monitoring pathogen virulence spectra, and the establishment of regionally based blast resistance breeding programs. To develop blast-resistant, high yielding rice varieties for Africa, we have established a breeding pipeline that utilizes real-time data of pathogen diversity and virulence spectra, to identify major and minor blast resistance genes for introgression into locally adapted rice cultivars. In addition, the project has developed a package to support sustainable rice production through regular stakeholder engagement, training of agricultural extension officers, and establishment of plant clinics.

Genetic diversity for drought and low-phosphorus tolerance in rice (Oryza sativa L.) varieties and donors adapted to rainfed drought-prone ecologies

Drought and phosphate availability are two major abiotic factors limiting productivity of rice in rainfed upland areas. There has been a constant need for new improved donor with tolerance to multiple abiotic stress conditions for rainfed rice breeding. In the present study, a set of 32 popular rice varieties and landraces were evaluated for drought and low-phosphorus (P) tolerance, and also characterized using grain yield under reproductive drought QTLs (DTY QTLs) and Pup1 linked/specific molecular markers. Twenty-seven genotypes were identified as tolerant to moderately tolerant to drought. The SSR markers linked to ten DTY QTLs classified the genotypes into two groups corresponding to aus and indica. The tolerant genotypes were distributed under both groups. Based on the core markers of Pup1 locus, complete tolerant haplotype was recorded in nine genotypes other than the tolerant check Dular. Nine more genotypes showed the incomplete tolerant haplotypes. The rice genotypes showed significantly high genetic variability for low-P tolerance in hydroponic study. A few genotypes revealed non-Pup1 type tolerance which needs further confirmation.

Unraveling candidate genomic regions responsible for delayed leaf senescence in rice

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).

Development of introgression lines in high yielding, semi-dwarf genetic backgrounds to enable improvement of modern rice varieties for tolerance to multiple abiotic stresses free from undesirable linkage drag

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.

Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker assisted breeding

Increases in rice productivity are significantly hampered because of the increase in the occurrence of abiotic stresses, including drought, salinity, and submergence. Developing a rice variety with inherent tolerance against these major abiotic stresses will help achieve a sustained increase in rice production under unfavorable conditions. The present study was conducted to develop abiotic stress-tolerant rice genotypes in the genetic background of the popular rice variety Improved White Ponni (IWP) by introgressing major effect quantitative trait loci (QTLs) conferring tolerance against drought (qDTY1.1, qDTY2.1), salinity (Saltol), and submergence (Sub1) through a marker assisted backcross breeding approach. Genotyping of early generation backcrossed inbred lines (BILs) resulted in the identification of three progenies, 3-11-9-2, 3-11-11-1, and 3-11-11-2, possessing all four target QTLs and maximum recovery of the recurrent parent genome (88.46%). BILs exhibited consistent agronomic and grain quality characters compared to those of IWP and enhanced performance against dehydration, salinity, and submergence stress compared with the recurrent parent IWP. BILs exhibited enhanced tolerance against salinity during germination and increased shoot length, root length, and vigor index compared to those of IWP. All three BILs exhibited reduced symptoms of injury because of salinity (NaCl) and dehydration (PEG) than did IWP. At 12 days of submergence stress, BILs exhibited enhanced survival and greater recovery, whereas IWP failed completely. BILs were found to exhibit on par grain and cooking quality characteristics with their parents. Results of this study clearly demonstrated the effects of the target QTLs in reducing damage caused by drought, salinity, and submergence and lead to the development of a triple stress tolerant version of IWP.

Genetic Diversity, Population Structure, and Marker-Trait Association for Drought Tolerance in US Rice Germplasm

Drought is a major constraint in some rice-growing areas of the United States. Its impact is most severe at the reproductive stage resulting in low grain yield. Therefore, assessment of genetic and phenotypic variation for drought tolerance in US rice germplasm is necessary to accelerate the breeding effort. Evaluation of 205 US rice genotypes for drought tolerance at the reproductive stage revealed tolerant response in rice genotypes Bengal, Jupiter, Cypress, Jazzman, Caffey, and Trenasse. Harvest index and fresh shoot weight were identified as important traits to explain the majority of variability among the genotypes under drought tolerance. Genotyping with 80 SSR markers indicated a low level of genetic diversity in US germplasm. Population structure analysis grouped the genotypes into eight clusters. The genotypes from California, Louisiana, and Arkansas formed distinct subgroups. Texas genotypes were similar to those from Louisiana and Arkansas. Marker-trait association analysis showed significant association of RM570 and RM351 with grain yield, spikelet fertility, and harvest index whereas shoot dry weight showed association with RM302 and RM461. The drought-tolerant genotypes identified in this study and the SSR markers associated with drought tolerance attributes will be helpful for development of improved drought-tolerant rice varieties through marker assisted selection.

Lectin Sequence Distribution in QTLs from Rice (Oryza sativa) Suggest A Role in Morphological Traits and Stress Responses

Rice (Oryza sativa) is one of the main staple crops worldwide but suffers from important yield losses due to different abiotic and biotic stresses. Analysis of quantitative trait loci (QTL) is a classical genetic method which enables the creation of more resistant cultivars but does not yield information on the genes directly involved or responsible for the desired traits. Lectins are known as proteins with diverse functions in plants. Some of them are abundant proteins in seeds and are considered as storage/defense proteins while other lectins are known as stress-inducible proteins, implicated in stress perception and signal transduction as part of plant innate immunity. We investigated the distribution of lectin sequences in different QTL related to stress tolerance/resistance, morphology, and physiology through mapping of the lectin sequences and QTL regions on the chromosomes and subsequent statistical analysis. Furthermore, the domain structure and evolutionary relationships of the lectins in O. sativa spp. indica and japonica were investigated. Our results revealed that lectin sequences are statistically overrepresented in QTLs for (a)biotic resistance/tolerance as well as in QTLs related to economically important traits such as eating quality and sterility. These findings contribute to the characterization of the QTL sequences and can provide valuable information to the breeders.

Overexpression of a phospholipase (OsPLDα1) for drought tolerance in upland rice (Oryza sativa L.)

This work aimed to evaluate the drought tolerance of transformed plants of the cultivar BRSMG Curinga that overexpress the rice phospholipase D α1 (OsPLDα1) gene. The productivity of independent transformation event plants of the OsPLDα1 gene was evaluated in an experiment where 19 days of water deficit were applied at the reproductive stage, a very strict growing condition for upland rice. The non-genetically modified cultivar (NGM) under drought treatment reduced productivity by 89% compared with that under irrigated treatment, whereas transformed plants (PLDα1_E2) reduced productivity by only 41%. After the drought treatment, the PLDα1_E2 plants productivity was five times greater than that of the NGM plant. Moreover, no adverse effects on growth and development of the transgenic plants were observed. Seven days after the resumption of irrigation, PLDα1_E2 plants had higher stomatal conductance, greater photosynthetic rate, and transpiration rate than did NGM plants, as well as a higher expression level of the OsPLDα1 gene. A delay in the senescence process was observed in these PLDα1_E2 plants, and this was determined for the recovery of photosynthesis, with greater expression of the Rubisco and lower expression of the SOD. This finding was suggestive of decreased oxidative stress, probably due to gas exchange by the partial closure of the stomata of these transformed plants, which prevented the formation of reactive oxygen species. OsPLDα1 gene overexpression resulted in a reduction in production loss under severe water deficit and revealed a possibility for the development of upland rice cultivars that are more tolerant to extreme drought conditions.

Genetic analysis of yield and agronomic traits under reproductive-stage drought stress in rice using a high-resolution linkage map

Drought stress at the reproductive stage of rice crop leads to a huge loss in grain yield. Identification and introgression of large effect drought tolerant QTLs are necessary to develop drought-tolerant rice varieties. Compared to the high-density linkage maps, widely spaced markers lead to the identification of QTLs with large confidence intervals which are difficult to incorporate in a breeding program. A previously generated genotyping-by-sequencing (GBS) based linkage map consisting of 4748 SNP markers was used to map QTLs in Cocodrie × N-22 recombinant inbred line (RIL) population. Twenty-one QTLs were discovered for days to flowering (DTF), plant height (PH), leaf rolling score (LRS), plant dry matter content (DM), spikelet fertility (SF), grain yield (GY), yield index (YI), and harvest index (HI) under drought stress. A major QTL qPH1.38 was identified in a narrow confidence interval on chromosome 1. The QTLs, qDTF3.01 and qPH1.38, overlapped with the previously identified QTL qDTY1.1 and Hd9, respectively. Another large-effect QTL qLRS1.37 was identified close to the sd1 locus on chromosome 1. A grain yield QTL qGY1.42 located on chromosome 1 contained only 4 candidate genes. There was no overlapping of QTLs for the root traits and the yield attributes. The important candidate genes present within the large effect QTL regions are MYB transcription factors, no apical meristem protein (NAC), potassium channel protein, nuclear matrix protein1, and chlorophyll A-B binding protein. The large effect QTLs (qDTF3.01, qPH1.38, and qLRS1.37) and a novel grain yield QTL qGYS1.42 can be used to incorporate in elite breeding lines to develop drought-tolerant rice varieties.

Physiological mechanisms contributing to the QTL qDTY3.2 effects on improved performance of rice Moroberekan x Swarna BC2F3:4 lines under drought

BACKGROUND

Traditional rice (Oryza sativa) varieties are valuable resources for the improvement of drought resistance. qDTY3.2 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 qDTY3.2. 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 qDTY3.2 since these phenotypes were consistently observed in the selected QTL lines with full introgression of qDTY3.2. We hypothesize that the qDTY3.2 associated RSA phenotypes led to better use of water and metabolic resources which, combined with earlier flowering time, improved yield under drought.

Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects

TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY3.1 , qDTY6.1 , and qDTY6.2 , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2-3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY6.1 and qDTY6.2 , respectively. QTL class analysis also showed that lines with a combination of qDTY3.1 and qDTY6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs.

Genetic Loci Governing Grain Yield and Root Development under Variable Rice Cultivation Conditions

Drought is the major abiotic stress to rice grain yield under unpredictable changing climatic scenarios. The widely grown, high yielding but drought susceptible rice varieties need to be improved by unraveling the genomic regions controlling traits enhancing drought tolerance. The present study was conducted with the aim to identify quantitative trait loci (QTLs) for grain yield and root development traits under irrigated non-stress and reproductive-stage drought stress in both lowland and upland situations. A mapping population consisting of 480 lines derived from a cross between Dular (drought-tolerant) and IR64-21 (drought susceptible) was used. QTL analysis revealed three major consistent-effect QTLs for grain yield (qDTY1.1, qDTY1.3 , and qDTY8.1 ) under non-stress and reproductive-stage drought stress conditions, and 2 QTLs for root traits (qRT9.1 for root-growth angle and qRT5.1 for multiple root traits, i.e., seedling-stage root length, root dry weight and crown root number). The genetic locus qDTY1.1 was identified as hotspot for grain yield and yield-related agronomic and root traits. The study identified significant positive correlations among numbers of crown roots and mesocotyl length at the seedling stage and root length and root dry weight at depth at later stages with grain yield and yield-related traits. Under reproductive stage drought stress, the grain yield advantage of the lines with QTLs ranged from 24.1 to 108.9% under upland and 3.0-22.7% under lowland conditions over the lines without QTLs. The lines with QTL combinations qDTY1.3 +qDTY8.1 showed the highest mean grain yield advantage followed by lines having qDTY1.1 +qDTY8.1 and qDTY1.1 +qDTY8.1 +qDTY1.3 , across upland/lowland reproductive-stage drought stress. The identified QTLs for root traits, mesocotyl length, grain yield and yield-related traits can be immediately deployed in marker-assisted breeding to develop drought tolerant high yielding rice varieties.

Genome-wide association mapping of canopy wilting in diverse soybean genotypes

KEY MESSAGE

Genome-wide association analysis identified 61 SNP markers for canopy wilting, which likely tagged 51 different loci. Based on the allelic effects of the significant SNPs, the slowest and fastest wilting genotypes were identified. Drought stress is a major global constraint for crop production, and slow canopy wilting is a promising trait for improving drought tolerance. The objective of this study was to identify genetic loci associated with canopy wilting and to confirm those loci with previously reported canopy wilting QTLs. A panel of 373 maturity group (MG) IV soybean genotypes was grown in four environments to evaluate canopy wilting. Statistical analysis of phenotype indicated wide variation for the trait, with significant effects of genotype (G), environment (E), and G × E interaction. Over 42,000 SNP markers were obtained from the Illumina Infinium SoySNP50K iSelect SNP Beadchip. After filtration for quality control, 31,260 SNPs with a minor allele frequency (MAF) ≥5% were used for association mapping using the Fixed and random model Circulating Probability Unification (FarmCPU) model. There were 61 environment-specific significant SNP-canopy wilting associations, and 21 SNPs that associated with canopy wilting in more than one environment. There were 34 significant SNPs associated with canopy wilting when averaged across environments. Together, these SNPs tagged 23 putative loci associated with canopy wilting. Six of the putative loci were located within previously reported chromosomal regions that were associated with canopy wilting through bi-parental mapping. Several significant SNPs were located within a gene or very close to genes that had a reported biological connection to transpiration or water transport. Favorable alleles from significant SNPs may be an important resource for pyramiding genes to improve drought tolerance and for identifying parental genotypes for use in breeding programs.

QTL Hotspots for Early Vigor and Related Traits under Dry Direct-Seeded System in Rice (Oryza sativa L.)

Strong seedling vigor is desirable trait in dry direct-seeded rice (DSR) for enhancing crop establishment and the ability to compete against weeds. A set of 253 BC3F4 lines derived from cross between Swarna and Moroberekan was phenotyped for early vigor (EV) and 8 related traits viz., early uniform emergence (EUE), shoot length (SHL), stem length (SL), shoot fresh weight (SFW), total fresh weight (TFW), shoot dry weight (SDW), total dry weight (TDW), and root dry weight (RDW). Composite interval mapping analysis using genotypic data from 194 SNP markers identified six genomic regions associated with traits on chromosomes 3, 4, 5, and 6 with phenotypic variance ranging from 2.5 to 18.6%. Among them 2 QTL regions; one on chr3 (id3001701-id300833) and the other on chr5 (wd5002636-id5001470) were identified as QTL hotspots A and B respectively and expressed consistently in field as well as glasshouse condition. The majority of QTLs identified for early vigor, and related traits were clustered in the QTL hotspots A (qEV3.1, qEUE3.1, qSHL3.1, qSL3.1, qSFW3.1, qTFW3.1, qRDW3.1 ) and QTL hotspot B (qEV5.1, qEUE5.1, qSHL5.1, qSL5.1, qSFW5.1, qSDW5.1, qTDW5.1 ). Ten putative candidate genes viz., 1-alpha-amylase precursor, 2-glutamate decarboxylase, 1-ethylene-insensitive 3, 3-expansin precursor, and 3-phenylalanine ammonia-lyase associated with the target traits were identified in the selected QTL regions. Mutations were identified in the coding region of alpha-amylase precursor and ethylene-insensitive 3 gene between the parents which can be utilized in marker assisted breeding. Trait relationships among the agro-physiological traits were examined to select the best genotypes for the given traits for use in future breeding programs.

Marker-assisted breeding to develop the drought-tolerant version of Sabitri, a popular variety from Nepal

Sabitri is a rice variety grown in a large part of the rainfed areas of Nepal. It was originally developed for irrigated condition; hence, this variety suffers high yield decline under drought. Two QTLs, qDTY_3.2 and qDTY_12.1 , with large effects on grain yield under drought were identified in the Sabitri background in separate QTL mapping studies. The present study reports the development of Sabitri near isogenic lines (NILs) with combinations of these two QTLs and their characterization under drought. To do so, marker-assisted backcross breeding (MABB) was combined with phenotypic selection to develop high-yielding drought-tolerant NILs with Sabitri grain type. Apart from this, drought-tolerant variants for grain type with high yield under non-stress were identified among the developed NILs. Early days to flowering of up to 13 days and reduction in plant height of up to 13 cm as compared to Sabitri were observed in the developed NILs. Some of these NILs showed higher yield compared to Sabitri and relatively higher tolerance to drought, indicating the capture of positive alleles and interactions during the course of selection. The developed NILs possessed high yield potential which make them suitable materials for the testing of water-saving technologies in irrigated areas. Based on their performance, these NILs can be deployed in rainfed areas in Nepal and other countries of South Asia to increase yield stability.

Molecular Mapping of QTLs Associated with Lodging Resistance in Dry Direct-Seeded Rice (Oryza sativa L.)

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 qCD_1.1 (with R² of 10%) and qCS_1.1 (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.

Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought

BACKGROUND

With the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selections were performed in every generation. BC1F3 derived pyramided lines (PLs) with different combinations of qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were evaluated under both RS and non-stress (NS) during the dry season (DS) of 2013 and 2014 at IRRI.

RESULTS

The GY reductions in RS trials compared to NS trials ranged from 79 to 99 %. Plant height (PH) was reduced and days to flowering (DTF) was delayed under RS. Eleven BC1F5 MRQ74 PLs with yield advantages of 1009 to 3473 kg ha(-1) under RS and with yields equivalent to MRQ74 under NS trials were identified as promising drought tolerance PLs. Five best PLs, IR 98010-126-708-1-4, IR 98010-126-708-1-3, IR 98010-126-708-1-5, IR 99616-44-94-1-1, and IR 99616-44-94-1-2 with a yield advantage of more than 1000 kg ha(-1) under RS and with yield potential equivalent to that of MRQ74 under NS were selected. The effect of three drought grain yield QTLs under RS in MRQ74 was validated. Under NS, PLs with two qDTY combinations (qDTY 2.2 + qDTY 12.1 ) performed better than PLs with other qDTY combinations, indicating the presence of a positive interaction between qDTY 2.2 and qDTY 12.1 in the MRQ74 background.

CONCLUSION

Drought tolerant MRQ74 PLs with a yield advantage of more than 1000 kg ha(-1) under RS were developed. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs.

Emerging tools, concepts and ideas to track the modulator genes underlying plant drought adaptive traits: An overview

Crop vulnerability to multiple abiotic stresses is increasing at an alarming rate in the current global climate change scenario, especially drought. Crop improvement for adaptive adjustments to accomplish stress tolerance requires a comprehensive understanding of the key contributory processes. This requires the identification and careful analysis of the critical morpho-physiological plant attributes and their genetic control. In this review we try to discuss the crucial traits underlying drought tolerance and the various modes followed to understand their molecular level regulation. Plant stress biology is progressing into new dimensions and a conscious attempt has been made to traverse through the various approaches and checkpoints that would be relevant to tackle drought stress limitations for sustainable crop production.

Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci

Background

Interaction and genetic control for traits influencing the adaptation of the rice crop to varying environments was studied in a mapping population derived from parents (Moroberekan and Swarna) contrasting for drought tolerance, yield potential, lodging resistance, and adaptation to dry direct seeding. A BC₂F₃-derived mapping population for traits related to these four trait groups was phenotyped to understand the interactions among traits and to map and align QTLs using composite interval mapping (CIM). The study also aimed to identify QTLs for the four trait groups as composite traits using multivariate least square interval mapping (MLSIM) to further understand the genetic control of these traits.

Results

Significant correlations between drought- and yield-related traits at seedling and reproductive stages respectively with traits for adaptation to dry direct-seeded conditions were observed. CIM and MLSIM methods were applied to identify QTLs for univariate and composite traits. QTL clusters showing alignment of QTLs for several traits within and across trait groups were detected at chromosomes 3, 4, and 7 through CIM. The largest number of QTLs related to traits belonging to all four trait groups were identified on chromosome 3 close to the qDTY_3.2 locus. These included QTLs for traits such as bleeding rate, shoot biomass, stem strength, and spikelet fertility. Multivariate QTLs were identified at loci supported by univariate QTLs such as on chromosomes 3 and 4 as well as at distinctly different loci on chromosome 8 which were undetected through CIM.

Conclusion

Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change. Understanding the genetics and trade-offs related to each of these environments and cultivation practices thus becomes highly important to develop varieties with stability of yield across them. This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments. With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0249-1) contains supplementary material, which is available to authorized users.

Composite Interval Mapping Based on Lattice Design for Error Control May Increase Power of Quantitative Trait Locus Detection

Experimental error control is very important in quantitative trait locus (QTL) mapping. Although numerous statistical methods have been developed for QTL mapping, a QTL detection model based on an appropriate experimental design that emphasizes error control has not been developed. Lattice design is very suitable for experiments with large sample sizes, which is usually required for accurate mapping of quantitative traits. However, the lack of a QTL mapping method based on lattice design dictates that the arithmetic mean or adjusted mean of each line of observations in the lattice design had to be used as a response variable, resulting in low QTL detection power. As an improvement, we developed a QTL mapping method termed composite interval mapping based on lattice design (CIMLD). In the lattice design, experimental errors are decomposed into random errors and block-within-replication errors. Four levels of block-within-replication errors were simulated to show the power of QTL detection under different error controls. The simulation results showed that the arithmetic mean method, which is equivalent to a method under random complete block design (RCBD), was very sensitive to the size of the block variance and with the increase of block variance, the power of QTL detection decreased from 51.3% to 9.4%. In contrast to the RCBD method, the power of CIMLD and the adjusted mean method did not change for different block variances. The CIMLD method showed 1.2- to 7.6-fold higher power of QTL detection than the arithmetic or adjusted mean methods. Our proposed method was applied to real soybean (Glycine max) data as an example and 10 QTLs for biomass were identified that explained 65.87% of the phenotypic variation, while only three and two QTLs were identified by arithmetic and adjusted mean methods, respectively.