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Recent predictions on climate change indicate that high temperature episodes are expected to impact rice production and productivity worldwide. The present investigation was undertaken to assess the yield stability of 72 rice hybrids and their parental lines across three temperature regimes over two consecutive dry seasons using the additive main effect and multiplicative interaction (AMMI), genotype and genotype × environment interaction (GGE) stability model analysis. The combined ANOVA revealed that genotype × environment interaction (GEI) were significant due to the linear component for most of the traits studied. The AMMI and GGE biplot explained 57.2% and 69% of the observed genotypic variation for grain yield, respectively. Spikelet fertility was the most affected yield contributing trait and in contrast, plant height and tiller numbers were the least affected traits. In case of spikelet fertility, grain yield and other yield contributing traits, male parent contributed towards heat tolerance of the hybrids compared to the female parent. The parental lines G74 (IR58025B), G83 (IR40750R), G85 (C20R) and hybrids [G21 (IR58025A × KMR3); G3 (APMS6A × KMR3); G57 (IR68897A × KMR3) and G41 (IR79156A × RPHR1005)] were the most stable across the environments for grain yield. They can be considered as potential genotypes for cultivation under high temperature stress after evaluating under multi location trials.

The consequences of climate change are drastically impacting field crop production; it is an immense prerequisite to attribute resilience through crop improvement. Thus, the breeders’ task is to su...

Phosphorus (P) is an essential macronutrient to all crops including rice and it plays a key role in various plant activities and development. Low availability of P in the soils negatively, influences rice crop growth and causes significant yield loss. In the present study, we characterized a set of 56 germplasm lines for their tolerance to low soil P by screening them at low soil P and optimum soil P levels along with low soil P tolerant and sensitive check varieties. These lines were genotyped for the presence/absence of tolerant allele with respect to the major low soil P tolerance QTL, Pup1, using a set of locus specific PCR-based markers, viz., K46-1, K46-2, K52 and K46CG-1. High genetic variability was observed for various traits associated with low soil P tolerance. The yield parameters from normal and low soil P conditions were used to calculate stress tolerance indices and classify the genotypes according to their tolerance level. Out of the total germplasm lines screened, 15 lines were found to be tolerant to low soil P condition based on the yield reduction in comparison to the tolerant check, but most of them harbored the complete or partial Pup1 locus. Interestingly, two tolerant germplasm lines, IC216831 and IC216903 were observed to be completely devoid of Pup1 and hence they can be explored for new loci underlying low soil P tolerance.

Jack (Artocarpus heterophyllus) is a multi-purpose out-breeding tree species of the family Moraceae. We generated 42,928,887 high-quality expressed sequence reads, assembled them into 89,356 unigenes, and discovered 16,853 unigene-based perfect SSRs in A. heterophyllus. Thirty-eight polymorphic SSRs were used to analyze the genetic diversity and population structure of 224 germplasm accessions of A. heterophyllus constituting three populations from three agro-climatic zones, namely Eastern Plateau and Hills, Middle Gangetic Plain Region, and Eastern Himalayan Region, encompassing five Eastern and North-Eastern states of India. At the 38 SSR loci, we detected 142 alleles with a mean of 3.74 alleles per locus. The PIC values for the loci ranged from 0.25 to 0.69. The maximum genetic diversity was recorded in Eastern Plateau and Hills (I = 0.98, He = 0.52). The ANOVA analysis indicated significantly higher within-population variation (90%) than between populations (10%). The indirect estimation of gene flow (Nm) from PhiPT indicated significant gene flow among all three populations. The population structure analysis showed at least four distinct groups among the three populations with different introgression degrees. The NJ-based clustering grouped the 224 germplasm accessions into three main clusters, each with three sub-clusters. However, we did not observe distinct geographical structure among populations except some clustering among the germplasm accessions of the populations of geographically close locations. The transcriptome dataset and the SSR markers developed in the study would boost the species' molecular characterization, conservation, and specific need-based improvement.

With an objective of mapping novel low soil P (Phosphorus) tolerance loci in the non-Pup1 type donor rice line, Wazuhophek, we screened a recombinant inbred line (RIL) mapping population consisting of 330 lines derived from the cross Wazuhophek x Improved Samba Mahsuri (which is highly sensitive to low soil P) in a plot with low soil P for tolerance associated traits. Molecular mapping with SSR markers revealed a total of 16 QTLs (seven major and nine minor QTLs), which are associated with low soil P tolerance related traits. Interestingly, a QTL hotspot, harbouring 10 out of 16 QTLs were identified on the short arm of chromosome 8 (flanked by the makers RM22554 and RM80005). Five major QTLs explaining phenotypic variance to an extent of 15.28%, 17.25%, 21.84%, 20.23%, and 18.50%, associated with the traits, plant height, shoot length, the number of productive tillers, panicle length and yield, respectively, were located in the hotspot. Two major QTLs located on chromosome 1, associated with the traits, total biomass and root to shoot ratio, explaining 15.44% and 15.44% phenotypic variance, respectively were also identified. Complex epistatic interactions were observed among the traits, grain yield per plant, days to 50% flowering, dry shoot weight, and P content of the seed. In-silico analysis of genomic regions flanking the major QTLs revealed the presence of key putative candidate genes, possibly associated with tolerance.

Improved-Samba-Mahsuri (ISM), a high-yielding, popular bacterial blight resistant (possessing Xa21, xa13, and xa5), fine-grain type, low glycemic index rice variety is highly sensitive to low soil phosphorus (P). We have deployed marker-assisted backcross breeding (MABB) approach for targeted transfer of Pup1, a major QTL associated with low soil P tolerance, using Swarna as a donor. A new co-dominant marker, K20-1-1, which is specific for Pup1 was designed and used for foreground selection along with functional markers specific for the bacterial blight resistance genes, Xa21, xa13, and xa5. A set of 66 polymorphic SSR marker were used for the background selection along with a pair of flanking markers for the recombination selection in backcross derived progenies and in BC2F2 generation, 12 plants, which are homozygous for Pup1, all the three bacterial blight resistance genes and possessing agro-morphological traits equivalent to or better than ISM were selected and selfed to produce BC2F3s. They were evaluated in plots with low soil P and normal soil P at ICAR-IIRR, Hyderabad for their low soil P tolerance, and bacterial blight resistance and superior lines were advanced to BC2F6. One of the lines, when tested at multiple locations in India was found promising under both normal as well as low soil P conditions.

A simple screening method is needed to identify rice genotypes tolerant to low phosphorus (P) in soil. Nagina 22 (N22) mutants were classified as gain of function (gof) and loss of function...

Influence of different phosphorus concentrations was studied in four rice varieties (Akhanphou, MTU1010, RP BIO 226, and Swarna) differing in their tolerance to low phosphorus. There was an increase in shoot and root dry mass with the increase in phosphorus concentration. At the low phosphorus concentration at both tillering and reproductive stages, Swarna, followed by Akhanphou, recorded maximum biomass for both roots and shoots, while the minimum was observed in RP BIO 226. Reduction in photosynthetic rate, stomatal conductance, transpiration rate, and internal CO2 concentration at low phosphorus concentrations were observed at both tillering and reproductive stages in all the genotypes. In low phosphorus, maximum photosynthetic rate was found in Swarna followed by Akhanphou. Phosphorus deficiency did not alter the maximum efficiency of PSII photochemistry, however, there was a reduction in effective PSII quantum yield, electron transport rate, and coefficient of photochemical quenching, while the coefficient of nonphotochemical quenching was higher in the low phosphorus-treated plants. Prolonged exposure to excessive energy and failure to utilize the energy in carbon-reduction cycle induced the generation of reactive oxygen species, which affected PSII as indicated by the fluorescence traits. The reduction was less severe in case of Swarna and Akhanphou. The activities of superoxide dismutase, peroxidase, and catalase increased in roots under low phosphorus concentration indicating that photoprotective mechanisms have been initiated in rice plants in response to phosphorus deficiency. Comparatively, Swarna and Akhanphou exhibited a higher biomass, higher photosynthetic rate, and better reactive oxygen species-scavenging ability which conferred tolerance under low phosphorus conditions.

Phosphorus (P) is an essential macro-nutrient required for growth and development of all crop plants including rice. Low availability of P in the soils manifests in terms of impeding crop growth leading to yield losses in rice. Adequate genetic variability for low soil P tolerance and also P use efficiency has been documented in rice and a major QTL called Pup1, conferring tolerance to low soil P has been identified, characterized and cloned from an Indian landrace, Kasalath. In the present study, a set of 98 germplasm lines collected from North-Eastern part of India were characterized for low soil P tolerance by screening them in a plot with low soil P (with available P 20 kg ha−1). The rice lines showed significantly high genetic variability for low soil P tolerance associated traits. Stress indices were estimated based on yield under normal and low soil P conditions and cluster analysis based on the stress indices; yield under normal and low soil P condition grouped the genotypes into highly tolerant, tolerant and sensitive to low soil P. Among the rice lines, 18 showed tolerance to low soil P (i.e. yield reduction

Phosphorus is one of the most limiting nutrients for plant growth in soil in both acidic and alkaline soils. To screen the genotypes for their P use efficiency and response to its application the genotypes need to be grown under different gradients so as to compare their performance under different regimes of P application. Therefore, low P plots were divided into 4 sub-plots with different gradients (0,20,40 and 60 kg P 2 O 5 /ha, respectively). Results showed that at 0 (absolute control) level of P 2 O 5 , rice genotypes differed widely among all the phenological and yield attributing characters studied. Root length measured was recorded lowest for Mahsuri cultivar (18cm) whereas highest root length at maturity stage was recorded for Vikas and Vasumati cultivars (26cm each). At 20 Kg P 2 O 5 /ha level, root length measured was recorded lowest for Mahsuri cultivar (19cm) whereas highest root length at maturity stage was recorded for Akshaydhan cultivar (30cm). At 40 Kg P 2 O 5 /ha level, root length measured was recorded lowest for MTU 1010 cultivar (20cm) whereas highest root length at maturity stage was recorded for Vasumati cultivar (30cm). Similarly At 60 Kg P 2 O 5 /ha level, for plant height the values ranged from a low of 58cm for Rp-bio-226 cultivar to a high of 99cm for Vardhan cultivar. Significant but not steep variations were noticed among cultivars for root length, flag leaf length and effective number of tillers characteristics at maturity stage.

The experiment was conducted out at the Indian Institute of Rice Research, Rajendranagar, Hyderabad during dry season (Rabi) 2013-2014 and Wet season (Kharif) 2014 crop seasons. The objective was to establish the nature of relation between grain yield and yield components by partitioning the correlation co-efficients between grain yield and its components into direct and indirect effects by using simple correlation and path analysis. A correlation co-efficient and path analysis study was conducted with eleven parents and their 24 F1 crosses for eleven component characters including grain yield. The correlation studies of these crosses showed that, grain yield per plant exhibited highly significant positive association with plant height, number of productive tillers per plant, panicle length, grains per panicle, and harvest index while days to 50 per cent flowering registered non-significant negative association with grain yield

MTU 1010 is a high-yielding mega-variety of rice grown extensively in India. However, it does not perform well in soils with low phosphorus (P) levels. With an objective to improve MTU 1010 for tolerance to low soil P, we have transferred Pup1, a major quantitative trait locus (QTL) associated with tolerance from another mega-variety, Swarna, through marker-assisted backcross breeding (MABB). Foreground selection of the F1 and backcross plants was performed with the co-dominant, closely linked CAPS marker, K20-2, while two flanking markers RM28011 and RM28157 were utilized for recombinant selection. At each backcross generation, positive plants were also analyzed with a set of 85 parental polymorphic SSR markers to identify the QTL-positive plants possessing maximum introgression of MTU 1010 genome. At BC2F1, the best backcross plant was selfed to generate BC2F2s. Among them, the plants homozygous for Pup1 (n = 22) were reconfirmed using the functional marker for Pup1, viz., K46-1, and they were advanced through pedigree method of selection until BC2F6 generation. A total of five elite BC2F6 lines, possessing Pup1 and phenotypically similar to MTU 1010, were screened in the low soil P plot and normal plot (with optimum soil P levels) during wet season, 2016. All the selected lines showed better performance under low P soil with more number of productive tillers, better root system architecture, and significantly higher yield (> 390%) as compared to MTU 1010. Further, under normal soil, the lines were observed to be similar to or better than MTU 1010 for most of the agro-morphological traits and yield. This study represents the successful application of marker-assisted selection for improvement of tolerance to low soil P in a high-yielding Indian rice variety.

Bacterial blight (BB) disease reduces the yield of rice varieties and hybrids considerably in many tropical rice growing countries like India. The present study highlights the development of durable BB resistance into the background of an elite maintainer of rice, DRR17B, by incorporating two major dominant genes, Xa21 and Xa33 through marker-assisted backcross breeding (MABB). Through two sets of backcrosses, the two BB resistance genes were transferred separately to DRR17B. In this process, at each stage of backcrossing, foreground selection was carried out for the target resistance genes and for non-fertility restorer alleles concerning the major fertility restorer genes Rf3 and Rf4, using gene-specific PCR-based markers, while background selection was done using a set of 61 and 64 parental polymorphic SSR markers respectively. Backcross derived lines possessing either Xa21 or Xa33 along with maximum genome recovery of DRR17B were identified at BC3F1 generation and selfed to develop BC3F2s. Plants harboring Xa21 or Xa33 in homozygous condition were identified among BC3F2s and were intercrossed with each other to combine both the genes. The intercross F1 plants (ICF1) were selfed and the intercross F2(ICF2) plants possessing both Xa21 and Xa33 in homozygous condition were identified with the help of markers. They were then advanced further by selfing until ICF4 generation. Selected ICF4 lines were evaluated for their resistance against BB with eight virulent isolates and for key agro-morphological traits. Six promising two-gene pyramiding lines of DRR17B with high level of BB resistance and agro-morphological attributes similar or superior to DRR17B with complete maintenance ability have been identified. These lines with elevated level of durable resistance may be handy tool for BB resistance breeding.

Rice is the most widely consumed staple food for a large part of the world’s human population, especially in Asia. Sheath blight caused by Rhizoctonia solani, is one of the most serious diseases of rice. Research progress is limited due to non availability of absolute resistant sources to sheath blight in rice. A total of 1013 germplasm comprising of mutants, introgression lines from wild species, A, B, R lines, Tropical japonica accessions, land races from north eastern India, wild rice accessions of O. nivara and O. rufipogon and gall midge biotype differentials maintained at ICAR-IIRR were evaluated with artificial inoculation for resistance to sheath blight disease during 2012 under field conditions. The germplasm identified as resistant/moderately resistant were further tested both under glass house and field conditions in the subsequent years (2013 and 2014) and seasons (Both Kharif and Rabi). Based on three years of testing, seven genotypes such as SM 801 (N 22 mutant), 10–3 (Introgression line), Ngnololasha, Wazuhophek, Gumdhan and Phougak (land races from north east) and RP 2068-18-3-5 (gall midge biotype differential) were identified as moderately resistant to sheath blight. Agro-morphological characterization using 62 DUS descriptors for two years (2013 and 2014) revealed that disease resistance positively correlated with stem thickness and negatively with tiller number. No correlation was observed with traits like plant height and heading date with sheath blight resistance. Resistant genotypes with medium to semi dwarf stature should be used in breeding programmes in the development of sheath blight resistant cultivars.

Forty-five rice lines comprising of thirty derived hybrid lines obtained from ten tropical Japonica, three Indica and two national checks viz. Pusa Basmati 1121 and Sarjoo-52 were evaluated for selection parameters, yield contributing components and genetic divergence. Fifteen quantitative and three qualitative traits were studied from experimentation with randomized block design during Kharif 2011. The phenotypic coefficient of variability was higher than genotypic coefficient of variability for all of the traits. The highest estimates of broad sense heritability coupled with genetic advance in per cent of mean was recorded for spikelets per panicle, plant height followed by L:B ratio, spikelets per panicle, grains per panicle, biological yield per plant, flag leaf area, days to 50% flowering, plant height which might be due to the additive nature of gene action. Such results indicated that these traits will be reliable for the effective selection. Highly positive and significant correlation was observed at both phenotypic and genotypic level between grain yield per plant and biological yield per plant, followed by panicle bearing tillers per plant, spikelet fertility, panicle length, 1000- grain weight, grains per panicle, panicle weight, flag leaf length, spikelet per panicle, flag leaf area, kernel length, flag leaf width, days to 50% flowering, and harvest index. This relationship reflected that grain yield and aforesaid economic traits can be increased simultaneously in breeding programme to develop high yielding Indica as well as Tropical Japonica rice varieties. Whole genotypes grouped in 8 non-overlapping clusters exhibited maximum genetic diversity between clusters III i.e., TJ- 64897 × NDR-359, TJ-64897 × CSR36, TJ-64897 × PB-1 and VIII i.e., TJ-11010 × NDR359, TJ-11010 × PB-1, TJ-16081 × NDR-359, TJ-16081 × PB-1. These clusters also stand for early days to flowering, short slender, second highest harvest index and panicle bearing tillers per plant, spikelets per panicle, grains per panicle, spikelet fertility, 1000- grain weight, long bold slender, biological yield per plant, and grain yield per plant. These genotypes showing higher mean performance for aforesaid traits can be exploited for enhancing hybrid vigour of desired New Plant Type with higher number of panicle bearing tillers per plant, spikelet per panicle and grains per spike in Indica as well as Tropical Japonica rice varieties for achieving higher yield. DOI: http://dx.doi.org/10.3329/sja.v11i2.18399 SAARC J. Agri., 11(2): 17-32 (2013)

Variations in leaf gas-exchange characteristics, leaf pigment content, and other important leaf traits were investigated in seven wild Oryza species, five hybrids, and five improved varieties. The significant variations were observed in photosynthetic pigment contents amongst different species of Oryza. The mean chlorophyll (Chl) content was higher in O. sativa (varieties and hybrids), while O. eichengeri showed the lowest Chl content. The mean carotenoid (Car) content in O. sativa (varieties and hybrids) was higher than in other wild rice species. O. eichengeri and O. barthii had significantly lower Car contents than other rice species. Significant differences were noticed in the rate of photosynthesis (P N), stomatal conductance (g s), transpiration rate (E), internal CO2 concentration (C i), specific leaf mass (SLM), and leaf thickness amongst different Oryza species. The mean P N was the highest in O. nivara followed by O. eichengeri. The mean P N was the lowest in O. glumaepatula, which was lower than that of cultivated varieties and hybrids of O. sativa. High rates of photosynthesis were observed in O. nivara (ACC. No. CR 100097), O. rufipogon (ACC.No. CR 100267), and O. nivara (ACC.No. CR 100008). The O. nivara and O. rufipogon genotypes with high P N might be used in rice improvement programmes for an increase of leaf photosynthesis in rice. Multiple correlations performed between different gas-exchange characteristics and other physiological traits revealed that the rate of photosynthesis was not dependent on the leaf pigment content or the leaf thickness. A strong positive correlation between P N and the P N/Ci ratio, which represents the carboxylation efficiency, indicated that the observed variation in P N was not based on pigment content or other leaf traits.

Manipur, a northeastern state of India lying in the Indo-Burmese biodiversity hot-spot is endowed with rich biodiversity of rice cultivars including those with medicinal values. The systematic evaluation of the indigenous cultivars for their grain and food qualities has not been carried out yet. Hence 13 indigenous medicinally used cultivars were subjected to grain and food quality studies. The cultivar, Naganap, has found to be of high protein type. Chinachang and Meriunap possessed strong scent comparable to Basmati 370. Most of them are of low and intermediate amylose (

DRR17A is a stable wild-abortive cytoplasmic male sterile line with medium-slender grain type. DRR17A and its maintainer line DRR17B are highly susceptible to two of the major rice diseases, bacterial blight (BB) and blast. To improve DRR17B for resistance against BB and blast, we have introgressed a major dominant gene each conferring resistance against BB (Xa21) and blast (Pi54) into the maintainer line through marker-assisted backcross breeding using RP-Bio-Patho-2 (a near-isogenic line of Samba Mahsuri possessing Xa21 and Pi54) as the donor parent. PCR-based molecular markers tightly linked to Xa21 and Pi54 were used for foreground selection of the resistance plants at each backcross generation, while molecular markers tightly linked to the major fertility restorer genes, Rf3 and Rf4, were used for negative selection (i.e. selection of plants possessing non-fertility-restoring alleles at the two loci) at BC1 generation. After foreground selection for the target genes at each backcross generation, the ‘positive’ plants were screened with parental polymorphic markers for identifying backcross plants possessing maximum recovery of DRR17B genome. Marker-assisted backcrossing was continued till BC3 generation, and a single BC3F1 plant possessing the target genes with ~94 % recovery of recurrent parent genome was identified and selfed to generate BC3F2s. A total of six homozygous BC3F2 plants were identified and advanced. At BC3F5, six promising, stable, backcross-derived lines possessing high level of resistance against BB and blast, high yield, short plant stature, fine-grain type, have been identified; their maintenance ability and heterotic potential validated through test crosses and these lines are being converted to CMS lines through marker-assisted breeding.

Farmers’ Rights are basically about enabling farmers to conserve, develop and utilise plant genetic resources and traditional knowledge and recognising and rewarding them for their contribution to the global genetic pool. The Convention on Biological Diversity recognised the sovereign rights of countries for use of these resources. It affirmed that the owners have rights of their innovations, associated traditional knowledge and traditional practices whether or not it can be protected by intellectual property rights. It is an obligation for the governments to protect the ownership of the resources and associated knowledge through legal policy or law. Subsequently, the International Treaty on Plant Genetic Resources for Food and Agriculture ensured the conservation and sustainable use of plant genetic resources and the equitable sharing of benefits from their use. Farmers’ Rights are a foundation stone of this Treaty, as their realisation is a precondition for the conservation and sustainable use of the world’s vital plant genetic resources and traditional knowledge. The Treaty recognises the enormous contribution that the farmers of all regions have made, and will continue to make, for the conservation and development of these resources throughout the world. It further stipulates that governments to protect and promote Farmers’ Rights and choose the measures to do so according to their needs and priorities.

Abiotic stresses such as drought, salt, heat, and cold are serious threats to the sustainability of rice yield. As rice is considered one of the major food crops, the development of enhanced abiotic stress tolerance using breeding and transgenic approaches will undoubtedly have a serious impact on global food security. Significant genetic variation in rice germplasm for resistance/tolerance to abiotic stresses makes plant breeding as a viable option of stress tolerance development. Though high-yielding rice cultivars with enhanced tolerance to abiotic stresses have been released, the progress made by conventional breeding was considerably slow due to multigenic nature of the traits and other associated problems. Biotechnology tools like molecular breeding and genetic engineering have accelerated the efforts of developing abiotic stress-tolerant crops. Further, the progress in identification of new genes and QTLs involved in abiotic stress response has supplemented the breeding and transgenic approaches of stress tolerance. The transgenic approach offers an alternative to breeding approaches for the genetic improvement of rice germplasm. In recent years, a number of stress-related genes have been identified and transferred in rice to improve its tolerance against abiotic stresses. Several transgenic rice lines with enhanced abiotic stress tolerance have been generated and evaluated. This chapter highlights the updates of breeding and transgenic approaches for the development of abiotic stress tolerance in rice with illustrations from research targeted at drought, salinity, heat, cold, and submergence.