Foreground Selection Research Articles

Deriving tropical gynoecious inbred backcross lines from exotic pickling cucumber using marker assisted backcross breeding

Indian cucumber cultivars are basically monoecious and vigorous in nature with many lateral branches but they are poor in productivity. The present study was aimed to introgress gynoecious trait (F locus) from pickling cucumber line (Gy14) into elite Indian cultivar Pusa Uday using marker assisted backcross breeding. Based on allelic diversity analysis, the allele numbers per locus ranged from 2 to 3 in BC1F3 and the observed heterozygosity (Ho) was ranged from 0.01 to 0.55. The heterozygosity expected (He) mean was 0.28 (range 0.03 to 0.50) which was higher than mean Ho (0.18) and mean polymorphic information content (PIC) for 87 markers was 0.23. Whereas the allele numbers per locus was 2 in BC2F2 and the observed heterozygosity (Ho) was ranged from 0.01 to 0.56. The mean expected heterozygosity (He) was 0.24 which was higher than mean Ho (0.17) and the mean PIC value was 0.19. The gynoecism (F locus) was introgressed in the Indian slicing cucumber cv. Pusa Uday though backcross breeding accompanied by foreground and background selections. The foreground selection was performed with one dominant SCAR marker, and 3 SSR markers (SSR 00233, SSR 15516 and SSR13251). A total of 87 polymorphic markers spanning genetic distance of 1031 cM with an average distance of 12.9 cM between adjacent markers were used for background selection. The genome recovery of the individuals in BC1F3 population was ranged from 62.64% to 93.10% while among BC2F2 plants it was ranged from 89.66% to 95.40%. Four inbred backcross lines (IBL) were selected from backcross populations (BC1F4 and BC2F3) those were purely gynoecious even at 45°C with more than 5 lateral branches. Hence, marker assisted backcross breeding served as a potential approach for precise introgression of the gynoecy (F locus) from picking cucumber to Indian slicing cucumber.

Development of Rice Varieties Adaptive to Nontidal Swampland using MABC: Growth Characteristics of Parent Plant and F1 Result

Lowland swamps have enormous potential and have been proven to provide significant contributions as a buffer in the national food security system. Rice farmers in non-tidal swamplands of South Sumatra plant rice at the end of the rainy season, because they wait for the water to recede, and therefore rice plants are very vulnerable to submerged stress in the vegetative phase and drought stress in the generative phase. This study aims to obtain rice varieties that are adaptive to these conditions and superior to lowland swamp agro-ecosystems. The research was conducted at the Plant Physiology Laboratory and Green House of Department of Agronomy, Faculty of Agriculture, Sriwijaya University. In this study, reciprocal crosses were carried out between Inpago 5 and Inpara 8 rice varieties. Inpago 5 variety was used because it has tolerant characters to drought stress in the generative phase and also has high production in farmers’ nontidal swampland. Inpara 8 has a Sub1 gene so that resistant to submerged stress in the vegetative phase. The results showed that both varieties had different characters in their growth and yield. Both varieties were crossed reciprocally and the success of crossing was more than 50%. F1 plants will be backcrossed with their female parents to get BC1F1 plants, and then selected using the MABC method [foreground selection, phenotypic selection, and background selection]. From the results of the MABC selection process, there will be BC1F1 plants with the genome proportion close to the female parent and confirmed to have the Sub1 gene.

Marker-Assisted Introgression and Stacking of Major QTLs Controlling Grain Number (Gn1a) and Number of Primary Branching (WFP) to NERICA Cultivars.

The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of them were cloned, only a few were utilized for actual systematic introgression breeding programs. In this study, the major yield QTLs Grain Number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP) were introgressed and stacked in selected NERICA cultivars by marker-assisted backcross breeding (MABB). The DNA markers RM3360, RM3452, and RM5493 were used for foreground selection. At BC3F4 and BC3F5 generation, a combination of marker-assisted selection and phenotypic evaluation were carried out to select lines with target alleles and traits. Further, genotyping-by-sequencing (GBS) was conducted to validate the introgression and determine the recurrent parent genome recovery (RPGR) of the selected lines. The Gn1a and/or WFP introgression lines showed significantly higher numbers of spikelets per panicle and primary branching compared to the recurrent parents. In addition, lines with Gn1a and/or WFP alleles were comparatively similar to the recurrent parents (RP) in most yield-related traits. This study demonstrates the success of utilizing yield QTLs and marker-assisted selection to develop and improve rice cultivars.

Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers.

The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC1F1 and BC2F1 individuals. Seven BC2F1 lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC2F2 grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC2F2 lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.

Improvement of rice cultivar for bacterial blight disease through marker assisted breeding approach

The present investigation was undertaken with the objective to develop high yielding, fine grain rice varieties possessing broad spectrum durable resistance by transferring bacterial leaf blight (BLB) resistant genes viz., xa13 and Xa21 from Improved Pusa Basmati 1. A popular high yielding and fine grain rice variety, HUBR 2-1 (Malviya Dhan 2-1), susceptible to BLB and Improved Pusa Basmati 1 carrying resistant genes for BLB (xa13 & Xa21 genes) were selected as parents for crossing. Improved Pusa Basmati 1 was verified for the presence of target genes by using gene linked primers viz., xa13 promotor and pTA 248. The cross viz., HUBR 2-1 x Improved Pusa Basmati 1 was undertaken during Kharif 2011 and F1 progenies were confirmed during rabi 2011. The F1 plants confirmed as true hybrids for both the genes were advanced to the F2 generation and foreground selection was done using gene linked markers. Genetic analysis in the F2 population confirmed that the genes (xa13 & Xa21) governing BLB resistance followed Mendelian inheritance. The phenotypic data analysis revealed that the plants carrying two resistance gene combinations (xa13xa13 Xa21Xa21, xa13xa13Xa21xa21) showed BLB resistance (0-3 scale), while the gene combinations viz., Xa13Xa13Xa21Xa21, Xa13Xa13Xa21xa21 and Xa13xa13Xa21Xa21, Xa13xa13Xa21xa21 showed BLB resistance (5-30).

Marker-assisted stacking of null Kunitz trypsin inhibitor and off-flavour generating lipoxygenase-2 in soybean

AbstractSoybean varieties genetically free from Kunitz trypsin inhibitor (KTI) and lipoxygenase-2 (Lox2) are desirable to increase human consumption, as the former is an antinutritional factor that affects protein digestibility while the latter is a principal contributor to off-flavour. In the present investigation, soybean genotypes free from both these undesirable components were developed by introgression of null allele of Lox2 from NRC109 (lox2lox2) into two KTI-free soybean genotypes derived from genotypes JS97-52 and NRC7. Foreground selection of plants in F1, F2, BC1F1, BC1F2, BC2F1 and BC2F2 generations developed from two cross combinations i.e. NRC7-derived KTI-free genotype (N7KTIF)×NRC109 (parental combination 1) and JS97-52 derived KTI free genotype (JKTIF)×NRC109 (parental combination 2) was performed using null allele specific markers and tightly linked simple sequence repeat (SSR) markers for both KTI and Lox2 genes for the identification of homozygous recessive (titilox2lox2) plants. Background selection was performed using 239 and 241 polymorphic SSR markers across the genome. This resulted in the development of 9 and 13 soybean lines stacked for null alleles of both KTI and Lox2 (titilox2lox2) exhibiting recurrent parent genome content more than 97 and 96%, respectively. Days-to-flowering, days-to-maturity, 100-seed weight and yield per plant of the stacked lines developed from both the parental combinations were at par with the respective recurrent parents.

First Indian Soybean Variety Free from Off-Flavour Generating Lipoxygenase-2 Gene Identified for Release for Commercial Cultivation

Soybean seed lipoxygenase-2 is the principal contributor to off-flavour associated with soy-products and constrains the utilization of soybean in food uses. A soybean genotype NRC132 genetically free from lipoxygenase-2 was developed through modified marker-assisted backcrossing by crossing climate-smart variety JS97-52 with null lipoxygenase-2 donor PI596540, an exotic germplasm accession. Null lipoxygenase-2 gene-specific marker and SSR marker linked to Lox2 locus were deployed for foreground selection and phenotyped through lipoxygenase-2 assay. The genotype was tested at multi-locations in Southern and Eastern zone in 2017, 2018, 2019 for yield and reaction to insect pests and diseases. The genotype yielded at par and significantly higher than the best performing check in Southern and Eastern zone, respectively, and showed resistance against potential diseases and insect pests at hotspots. Soy-milk produced from NRC132 gave reduced off-flavour. The genotype identified for release as variety holds potential to boost utilization of soybean in manufacturing food products.

Weakly supervised object-aware convolutional neural networks for semantic feature matching

We address the task of establishing visual correspondences between two images depicting main objects of the same semantic category. This task encounters various challenges such as background clutter, intra-class variation, and viewpoint variations. Existing works are dominated by end-to-end training methods that rely on redundant calculation or large amounts of manual annotations, and cannot generalize to unseen object categories. In this paper, we propose to construct a weakly supervised object-aware convolutional neural network architecture for semantic feature matching, while being trainable end-to-end without the requirement for manual annotations. The main component of this architecture is a similarity filter module containing a trainable neural nearest neighbors network. Since training data for semantic feature matching is rather limited, we introduce a simple and effective foreground selection strategy to produce the foreground masks. Using these masks as a form of weak supervision signal for correspondence task and tackle the background clutter. Extensive experiments illustrate that the proposed approach outperforms the state-of-the-art methods for semantic feature matching on multiple public standard benchmark datasets.

Enhancing backcross programs through increased recombination

BackgroundIntrogression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters.ResultsIn this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental.ConclusionsDepending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation.

Marker-assisted gene pyramiding (MAGP) for semi dwarfed bacterial blight resistance genes into traditional basmati variety “Ranbir Basmati”

Evolution of new virulent races has led to increased sensitiveness of the traditional basmati varieties to bacterial blight (BB) disease. Among the traditional basmati varieties, Ranbir Basmati is tall statured variety, and are susceptible to BB diseases. The variety has thin stem and prone to lodging leading to significant yield losses as well as deteriorate the grain qualities. In the present study, the marker-assisted backcross breeding (MABB) strategy were used for simultaneous stepwise transfer of two major BB resistance genes (Xa21 and xa13) along with a dwarfing gene (sd1) into Ranbir Basmati. The molecular markers viz., pTA 248, xa13prom and h linked to Xa21, xa13 and sd1, respectively were used in MABB programme. Both foreground and background selection approaches are used for pyramiding of genes of interest into Ranbir Basmati. The crosses were attempted for pyramiding the BB resistance genes along with dwarfing gene from Punjab Basmati 4 (Xa21, xa13 and sd1) into Ranbir Basmati. MABB programme was carried out up to BC2F5 generations. In total five semi-dwarf pyramided lines namely, SBTIL25, SBTIL39, SBTIL80, SBTIL121 and SBTIL31 have been identified for further field screening. These pyramided lines possess superior length/width ratio, excellent cooking properties and pleasant aroma. These five lines have been further evaluated for morpho-physiological and quality traits, and can be serve as potential donors for different rice pre-breeding programmes. These promising pyramided lines in bulk will be subjected to testing in multi-location and replicated trial for yield and disease resistance for their possible release as variety.

Introgression of "QTL-hotspot" region enhances drought tolerance and grain yield in three elite chickpea cultivars.

With an aim of enhancing drought tolerance using a marker-assisted backcrossing (MABC) approach, we introgressed the "QTL-hotspot" region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought-tolerance related traits into three elite Indian chickpea (Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92-3. Of eight simple sequence repeat (SSR) markers in the QTL-hotspot region, two to three polymorphic markers were used for foreground selection with respective cross-combinations. A total of 47, 53, and 46 SSRs were used for background selection in case of introgression lines (ILs) developed in genetic backgrounds of Pusa 372, Pusa 362, and DCP 92-3, respectively. In total, 61 ILs (20 BC3 F3 in Pusa 372; 20 BC2 F3 in Pusa 362, and 21 BC3 F3 in DCP 92-3), with >90% recurrent parent genome recovery were developed. Six improved lines in different genetic backgrounds (e.g. BGM 10216 in Pusa 372; BG 3097 and BG 4005 in Pusa 362; IPC(L4-14), IPC(L4-16), and IPC(L19-1) in DCP 92-3) showed better performance than their respective recurrent parents. BGM 10216, with 16% yield gain over Pusa 372, has been released as Pusa Chickpea 10216 by the Central Sub-Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India. In summary, this study reports introgression of the QTL-hotspot for enhancing yield under rainfed conditions, development of several introgression lines, and release of Pusa Chickpea 10216 developed through molecular breeding in India.

Introgression of qDTY1.1 Governing Reproductive Stage Drought Tolerance into an Elite Basmati Rice Variety “Pusa Basmati 1” through Marker Assisted Backcross Breeding

Drought stress at the reproductive stage in rice is one of the most important cause for yield reduction, affecting both productivity and quality. All Basmati rice varieties, including the popular cultivar “Pusa Basmati 1 (PB1)” is highly sensitive to reproductive stage drought stress (RSDS). We report for the first time, improvement of a Basmati cultivar for RSDS tolerance, with the introgression of a major quantitative trait locus (QTL), “qDTY1.1” into PB1. The QTL was sourced from an aus variety, Nagina 22 (N22). A microsatellite (simple sequence repeat (SSR)) marker “RM 431” located at telomeric end (38.89 mb) of chromosome 1, and located within a 1.04 mb QTL region was employed for foreground selection for qDTY1.1 in the marker assisted backcross breeding process. A set of 113 SSR markers polymorphic between N22 and PB1 were utilized for background selection to ensure higher recurrent parent genome recovery. After three backcrosses followed by five generations of selfing, eighteen near isogenic lines (NILs) were developed, through combinatory selection for agro-morphological, grain and cooking quality traits. The NILs were evaluated for three consecutive Kharif seasons, 2017, 2018 and 2019 under well-watered and drought stress conditions. RSDS tolerance and yield stability indicated that P1882-12-111-3, P1882-12-111-5, P1882-12-111-6, P1882-12-111-7, P1882-12-111-12, P1882-12-111-15 and P1882-12-111-17 were best in terms of overall agronomic and grain quality under RSDS. Additionally, NILs exhibited high yield potential under normal condition as well. The RSDS tolerant Basmati NILs with high resilience to water stress, is a valuable resource for sustaining Basmati rice production under water limiting production environments.

Drought Tolerant near Isogenic Lines (NILs) of Pusa 44 Developed through Marker Assisted Introgression of qDTY2.1 and qDTY3.1 Enhances Yield under Reproductive Stage Drought Stress

Reproductive stage drought stress (RSDS) is detrimental for rice, which affects its productivity as well as grain quality. In the present study, we introgressed two major quantitative trait loci (QTLs), namely, qDTY2.1 and qDTY3.1, governing RSDS tolerance in a popular high yielding non-aromatic rice cultivar, Pusa 44, through marker-assisted backcross breeding (MABB). Pusa 44 is highly sensitive to RSDS, which restricts its cultivation across drought-prone environments. Foreground selection was carried out using markers, RM520 for qDTY3.1 and RM 521 for qDTY2.1. Background selection was achieved with 97 polymorphic SSR markers in tandem with phenotypic selection to achieve faster recurrent parent genome (RPG) recovery. Three successive backcrosses followed by three selfings aided RPG recoveries of 98.6% to 99.4% among 31 near isogenic lines (NILs). Fourteen NILs were found to be significantly superior in yield and grain quality under RSDS with higher drought tolerance efficiency (DTE) than Pusa 44. Among these, the evaluation of two promising NILs in the multilocational trial during Kharif 2019 showed that they were significantly superior to Pusa 44 under reproductive stage drought stress, while performing on par with Pusa 44 under normal irrigated conditions. These di-QTL pyramided drought-tolerant NILs are in the final stages of testing the All India Coordinated Rice Improvement Project varietal trials for cultivar release. Alternately, the elite drought-tolerant Pusa 44 NILs will serve as an invaluable source of drought tolerance in rice improvement.

Marker Assisted Gene Pyramiding for Bacterial Blight Resistance in Some Improved Rice Genotypes

Bacterial blight is one of the major diseases of rice, causing huge economic loss to the rice farmers around the world. In the present study, marker assisted selection (MAS) was used to pyramid broad spectrum resistance genes (Xa33 and Xa38) into two improved rice genotypes (ADT 47 and ASD 16) which already have some bacterial blight resistance genes (xa5, xa13 and Xa21). The rice genotypes FBRI-15 and PR114 were used as donors of Xa33 and Xa38 genes respectively. The marker RMWR7.1 linked to Xa33 and the sequenced-tagged site marker Os04g53050-1 specific to Xa38 were used for foreground selection. True F1 hybrids were selected using the polymorphic markers. Out of one hundred and thirty-seven SSR markers, forty-two were polymorphic for improved ADT 47 x FBRI-16 and forty-six were polymorphic for Improved ASD 16 x PR114. The polymorphic markers were used for background selection. Foreground selection revealed that a single F1 plant was heterozygote in Improved ADT 47 X FBRI-15 whereas two plants were heterozygotes in Improved ASD 16 x PR114. At BC1F1, one and three plants were found to be heterozygous respectively for Improved ADT 47 x FBRI-15 and Improved ASD 16 x PR114. At BC2F1, single plant each was found heterozygous from the two crosses. In the final BC3F1 population, one heterozygote each was obtained from the two crosses. In BC3F1, plant number 11 had 92.80% parental genome recovery in the Improved ADT 47 x FBRI-15, whereas plant no 16 had 91.33% parental genome recovery in the Improved ASD 16 x PR114

Rapid genotyping of bacterial leaf blight resistant genes of rice using loop-mediated isothermal amplification assay.

The use of resistant (R) genes is the most effective strategy to manage bacterial leaf blight (BLB) disease of rice. Several attempts were made to incorporate R genes into susceptible rice cultivars using marker-assisted backcross breeding (MABB). However, MABB relies exclusively on PCR for foreground selection of R genes, which requires expensive equipment for thermo-cycling and visualization of results; hence, it is limited to sophisticated research facilities. Isothermal nucleic acid amplification techniques such as loop-mediated isothermal amplification (LAMP) assay do not require thermo-cycling during the assay. Therefore, it will be the best alternative to PCR-based genotyping. In this study, we have developed a LAMP assay for the specific and sensitive genotyping of seven BLB resistance (R) genes viz., Xa1, Xa3, Xa4, Xa7, Xa10, Xa11, and Xa21 in rice. Gene-specific primers were designed for the LAMP assay. The LAMP assay was optimized for time, temperature, and template DNA concentration. For effective detection, incubation at 60°C for 30min was optimum for all seven R genes. A DNA intercalating dye ethidium bromide and a calorimetric dye hydroxynaphthol blue was used for result visualization. Further, sensitivity assay revealed that the LAMP assay could detect R genes at 100fg of template DNA compared to 1ng and 10pg, respectively, in conventional PCR and q-PCR assays. The LAMP assay developed in this study provides a simple, specific, sensitive, robust, and cost-effective method for foreground selection of R genes in the resistance breeding programs of resource-poor laboratory.

Introgression of rice blast and bacterial leaf blight resistance genes into HPR2143 rice variety through marker assisted selection and Anther culture

The use of resistant rice cultivars is the most proficient way to overcome rice blast and bacterial blight diseases in rice. Cultivars, however, experience a rapid breakdown in their resistance, predominantly due to the advent of new pathotypes. Therefore, for durable resistance, it is important to combine multiple genes that impart resistance to more than one pathotypes into one genetic background. Foreground selection of BC2F2 plants of two crosses (HPR2143/DHMAS164 and HPR2143/PB1) was done to detect the presence of blast resistance genes i.e. Pita and Pi9 in these plants. Plants homozygous for gene Pita were screened by a pair of gene specific markers YL87/155 (coupling dominant) and YL87/183 (repulsion dominant). Likewise, homozygous positive plants for gene Pi9 were identified using the co-dominant marker Pi9STS-1. For bacterial blight (BLB) resistance genes, BC2F2 plants of two crosses (HPR2143/IRBB54 and HPR2143/PR114) were screened for genes Xa21 and Xa38 using gene-derived markers BLB248 and Oso4g53050-1, respectively. Anther culture of developed F1s was attempted for fixation of genes.

Battling against Brown Planthopper in Rice: Genomic Selection in Backcross Breeding to Produce Resistant Cultivars - A Review

Brown Planthopper (BPH), Nilaparvata lugens Stål, imposes a significant threat to the rice cultivation in Sri Lanka, generating 5–10% of annual yield losses. Rice farmers mainly adopt chemical methods to control the BPH attacks. The intensive use of insecticides is a crucial trigger for the development of resistance and hence continuous BPH outbreaks. Thus, the chemical methods of control do not provide a permanent solution to the BPH. The most recommended strategy of resolving the BPH crisis in rice is the development of resistant cultivars. Most of the Sri Lankan rice germplasm has already been screened for BPH resistance; however, reliable molecular breeding strategies must be implemented to acieve this target. Development of BPH resistant cultivars relies on utilizing appropriate genomic selection protocols in breeding schemes such as marker-assisted backcrossing. Therefore, a literature survey was carried out to evaluate BPH control methods and to emphasize the employment of backcross breeding with the genomic selection approach as a precise tool to develop BPH resistant rice varieties. The genetic basis of BPH resistance has been unravelled for many rice cultivars however, further screening is required to identify locally available resistant sources. The polymorphic markers for the foreground and background selection must be developed for the introgression of the BPH resistant genes and recovery of the recurrent parent genome. The validation of the markers developed in the international breeding and genetics programmes for the local germplasm is also an essential step prior to the genomic selection of BPH resistant rice varieties.

Marker assisted improvement of low soil phosphorus tolerance in the bacterial blight resistant, fine-grain type rice variety, Improved Samba Mahsuri

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.

Pyramiding Ty-1/Ty-3, Ty-2, ty-5 and ty-6 genes into tomato hybrid to develop resistance against tomato leaf curl viruses and recurrent parent genome recovery by ddRAD sequencing method

Tomato leaf curl virus (ToLCV) is a begomovirus transmitted by whitefly (Bemisia tabaci) and causes Tomato (yellow) leaf curl disease (TYLCD/ToLCD) in many parts of India and rest of the world resulting in huge economic losses. Many Ty genes identified either from wild and/or cultivated tomato, which confers various levels of resistance to ToLCV. The current study aimed at stacking four important resistant genes (Ty-1/Ty-3, Ty-2, ty-5, and ty-6) in parental lines of a commercial tomato hybrid JKTH811 with the aid of the marker-assisted backcross breeding program. As a donor source, two pre-breeding lines, CLN3125K (Ty-1/Ty-3 and Ty-2) and FLA456 (ty-5 and ty-6) was used. Crossed population screened by using tightly linked Ty genes specific markers for foreground selection and attempted the fastest recovery of recurrent parental genome through NGS based ddRAD sequencing approach. Ty genes introgressed parental lines as well as the resulting F1 hybrids were tested for their bio-efficacy against ToLCNDV (New Delhi var.) under greenhouse and field conditions. Disease severity of Ty genes pyramided female lines and F1 hybrids were found as significantly lower when compared to original parental lines and hybrid. This report demonstrates the efficiency of Ty genes pyramiding from different donors in a hybrid against ToLCV and recovery of the recurrent genome using the ddRAD-seq platform in the minimum generations possible.

Genetic enhancement of essential amino acids for nutritional enrichment of maize protein quality through marker assisted selection.

Maize grain protein is deficient in two essential amino acids, lysine and tryptophan, defining it as of low nutritive value. The discovery of opaque2 (o2) gene has led to the development of quality protein maize (QPM) that has enhanced levels of essential amino acids over normal maize. However, the adoption of QPM is still very limited. The present study aims at improving the quality of normal four maize inbred lines (LM11, LM12, LM13 and LM14) of single cross hybrids; Buland (LM11 × LM12) and PMH1 (LM13 × LM14) released in India for different agro-climatic zones by introgressing o2 allele along-with modifiers using marker assisted backcross breeding. Both foreground and background selection coupled with phenotypic selection were employed for selection of o2 specific allele and maximum recovery of the recurrent parent genome (87-90%) with minimum linkage drag across the crosses. The converted QPM lines had <25% opaqueness which isclose to the respective recurrent parents. The QPM versions showed high level of tryptophan content ranging from 0.72 to 1.03 across the four crosses. The newly developed best QPM lines were crossed in original combinations to generate QPM hybrids. The grain yield of improved QPM hybrids was at par and there was significant increase in tryptophan content over the original hybrids.The integrated marker assisted, and phenotypic selection approach holds promise to tackle complex genetics of QPM. The dissemination and adoption of improved QPM versions may help to counteract protein-energy malnutrition in developing countries.