R. Chandra Babu

Assessment of Genetic Diversity among Finger Millet (Eleusine coracana (L.) Gaertn.) Accessions using Molecular Markers

Finger millet (Eleusine coracana), an allotetraploid cereal, is widely cultivated in the arid and semiarid regions of the world. Being rich in protein and calcium, finger millet serves as an important staple food for rural populations in developing tropical countries where calcium deficiency and anemia are wide spread. Thirty-two finger millet genotypes were fingerprinted using 50 random amplified polymorphic DNA (RAPD) markers. Out of the total 529 loci generated using the 50 RAPD primers, 479 loci (91%) were polymorphic and informative to differentiate the accessions. Cluster analysis grouped the 32 finger millet accessions into two major clusters. Among the 32 finger millet genotypes, GEC 182 and CO 12 were distantly related with a low similarity index of 0.315. These two accessions also differed considerably in days to flowering and grain weight; GEC 182 is early flowering and has bold grains, while CO 12 is late flowering and has smaller grains. These two accessions with higher diversity at molecular level, phenology and grain weight will be ideal as parents in hybridization programme, to develop improved finger millet varieties suitable for peninsular region of India.

QTLs linked to leaf epicuticular wax, physio-morphological and plant production traits under drought stress in rice (Oryza sativa L.)

Drought stress is the major constraint to rice (Oryza sativa L.) production and yield stability in rainfed ecosystems. Identifying genomic regions contributing to drought resistance will help to develop rice cultivars suitable for rainfed regions through marker-assisted breeding. Quantitative trait loci (QTLs) linked to leaf epicuticular wax, physio-morphological and plant production traits under water stress and irrigated conditions were mapped in a doubled haploid (DH) line population from the cross CT9993-5-10-1-M/IR62266-42-6-2. The DH lines were subjected to water stress during anthesis. The DH lines showed significant variation for epicuticular wax (EW), physio-morphological and plant production traits under stress and irrigated conditions. A total of 19 QTLs were identified for the various traits under drought stress and irrigated conditions in the field, which individually explained 9.6%–65.6% of the phenotypic variation. A region EM15_10-ME8_4-R1394A-G2132 on chromosome 8 was identified for leaf EW and rate of water loss i.e., time taken to reach 70% RWC from excised leaves in rice lines subjected to drought stress. A large effect QTL (65.6%) was detected on chromosome 2 for harvest index under stress. QTLs identified for EW, rate of water loss from excised leaves and harvest index under stress in this study co-located with QTLs linked to shoot and root-related drought resistance traits in these rice lines and might be useful for rainfed rice improvement.

Mapping Consistent Rice (Oryza sativa L.) Yield QTLs under Drought Stress in Target Rainfed Environments.

BackgroundDrought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target production environments, as well as across different genetic backgrounds, will help to develop high-yielding rice cultivars suitable for water-limited environments through marker-assisted breeding (MAB). Considerable progress has been made in mapping QTLs for drought resistance traits in rice; however, few have been successfully used in MAB.ResultsRecombinant inbred lines of IR20 × Nootripathu, two indica cultivars adapted to rainfed target populations of environments (TPEs), were evaluated in one and two seasons under managed stress and in a rainfed target drought stress environment, respectively. In the managed stress environment, the severity of the stress meant that measurements could be made only on secondary traits and biomass. In the target environment, the lines experienced varying timings, durations, and intensities of drought stress. The rice recombinant inbred lines exhibited significant genotypic variation for physio-morphological, phenological, and plant production traits under drought. Nine and 24 QTLs for physio-morphological and plant production traits were identified in managed and natural drought stress conditions in the TPEs, respectively. Yield QTLs that were consistent in the target environment over seasons were identified on chromosomes 1, 4, and 6, which could stabilize the productivity in high-yielding rice lines in a water-limited rainfed ecosystem. These yield QTLs also govern highly heritable key secondary traits, such as leaf drying, canopy temperature, panicle harvest index and harvest index.ConclusionThree QTL regions on chromosome 1 (RM8085), chromosome 4 (I12S), and chromosome 6 (RM6836) harbor significant additive QTLs for various physiological and yield traits under drought stress. The similar chromosomal region on 4 and 6 were found to harbor QTLs for canopy temperature and leaf drying under drought stress conditions. Thus, the identified large effect yield QTLs could be introgressed to develop rice lines with stable yields under varying natural drought stress predominant in TPEs.

Mapping QTLs for Plant Phenology and Production Traits Using Indica Rice ( Oryza sativa L.) Lines Adapted to Rainfed Environment

Drought is a major abiotic stress limiting rice production and yield stability in rainfed ecosystems. Identifying quantitative trait loci (QTL) for rice yield and yield components under water limited environments will help to develop drought resilient cultivars using marker assisted breeding (MAB) strategy. A total of 232 recombinant inbred lines of IR62266/Norungan were used to map QTLs for plant phenology and production traits under rainfed condition in target population of environments. A total of 79 QTLs for plant phenology and production traits with phenotypic variation ranging from 4.4 to 72.8% were detected under non-stress and drought stress conditions across two locations. Consistent QTLs for phenology and production traits were detected across experiments and water regimes. The QTL region, RM204–RM197–RM217 on chromosome 6 was linked to days to 50% flowering and grain yield per plant under both rainfed and irrigated conditions. The same genomic region, RM585–RM204–RM197 was also linked to harvest index under rainfed condition with positive alleles from Norungan, a local landrace. QTLs for plant production and drought resistance traits co-located near RM585–RM204–RM197–RM217 region on chromosome 6 in several rice genotypes. Thus with further fine mapping, this region may be useful as a candidate QTL for MAB, map-based cloning of genes and functional genomics studies for rainfed rice improvement.

Depth of soil compaction predominantly affects rice yield reduction by reproductive-stage drought at varietal screening sites in Bangladesh, India, and Nepal

AimsDrought is the major constraint to rainfed rice productivity in South Asia, but few reports provide detailed characterization of the soil properties related to drought stress severity in the region. The aim of the study was to provide a compilation of drought breeding network sites and their respective levels of drought stress, and to relate soil parameters with yield reduction by drought.MethodsThis study characterized levels of drought stress and soil nutrient and physical properties at 18 geographically distributed research station sites involved in rice varietal screening in Bangladesh, India, and Nepal, as well as at farmers’ fields located near the research stations.ResultsBased on soil resistance to penetration profiles, a hardpan was surprisingly absent at about half of the sites characterized. Significant relationships of depth of compaction and yield reduction by drought indicated the effects of soil puddling on susceptibility to cracking, rather than water retention by hardpans, on plant water availability in this region. The main difference between research stations and nearby farmers’ fields was in terms of soil compaction.ConclusionsThese results present an initiative for understanding the range of severities of reproductive-stage drought stress in drought-prone rainfed lowland rice-growing areas in South Asia.

Identification of elite lines and consistent markers linked to yield and yield components in rice (Oryza sativa L.) using association mapping

Genetic variation is the foundation of crop improvement. Identifying donors for yield and yield components will help to develop high yielding cultivars. Yield being a complex trait, understanding its molecular genetics may hasten breeding for high yield. Identifying molecular markers associated with yield traits will improve efficiency of breeding. Forty-nine diverse rice genotypes were evaluated for yield and yield components under irrigated conditions in three separate field trials at Paddy Breeding Station, Coimbatore during February – June, 2014, August – December, 2014 and 2015. Significant variation for yield and yield-related traits was noticed among the genotypes. IR58821 and IR52561 gave consistently higher yield in three and two trials, respectively. Association mapping detected a total of 46 markers associated with growth and yield traits. PSM432, PSM371A and PSM167 were consistently associated with yield and harvest index. IR58821 and IR52561 and markers consistently associated with yield traits may help to develop improved rice cultivars through marker assisted breeding.

Identification of microsatellite markers linked to drought tolerance in rice (Oryza sativa L.) through bulked line analysis

Identification of donor parents and markers for traits conferring drought tolerance eventually hastens the breeding for drought tolerance in rice. The extent of variation for water stress indicators, physio-morphological and plant production traits were assessed by evaluating 36 rice genotypes under water stress condition. Significant variation was observed for these traits and thirteen drought tolerant and susceptible genotypes were selected and grouped as tolerant and susceptible bulks based on physio-morphological and biochemical characterization. Genomic DNA was isolated from these rice accessions and pooled, respectively into drought tolerant and susceptible bulks. Bulked line analysis was carried to identify microsatellite markers linked to drought tolerance in rice. Out of 200 SSR primers screened RM 1092; RM 129 and RM157B were polymorphic between the bulks and also co-segregated among the individual genotypes constituting the respective bulks. The genomic regions flanked by these markers have been identified to be associated with various drought tolerance traits in rice and can be useful for marker assisted selection for drought resistance improvement in rice. The genotypes identified as drought tolerant can be used us donars in drought improvement breeding programmes. Key words Rice, drought resistance, microsatellite markers, bulk line analysis

Genetic analysis of yield traits in rice under irrigated and water stress environments

Experiments were conducted to study the genetics and combining ability for yield and its components under irrigated (E I) and water stress environments (E II) using F1 hybrids derived from a full diallel mating involving four drought tolerant and four drought sensitive rice genotypes. Significant differences were observed for all the traits studied in both EI and EII environments, except harvest index in E II. Additive and non-additive gene actions for days to flowering, biomass and harvest index and nonadditive gene action for grain yield in both the environments were observed. Importance of additive gene action in E I and non-additive gene action in E II was observed for grains panicle–1, whereas shift in non-additive to additive from E I to E II was observed for productive tillers plant−1. The significance of gca and gca x environment interaction indicated the differential contribution of parents for days to flowering, biomass and harvest index. Based on the mean values and gca effects, landraces Nootripathu and Norungan were adjudged as the potential parents to improve grain yield under stress, where as CO43 and IR62266 were identified as good general combiners to improve grain yield and its component traits under irrigated environment. The hybrids viz., PMK2/CO43, CO43/Nootripathu, Nootripathu/Kallurundaikar, Norungan/IR64, Kallurundaikar x PMK2 and IR20 x IR62266 were identified as superior ones for improving yield under water stress.