Foreground Selection Research Articles

Molecular Evaluation for Drought Tolerant Using Marker Assisted Breeding Method

The sustainability and increasing the national rice production require the readiness of food and agriculture sector cope with the impacts of climate change, land degradation, drought area, sloping production and the raising of population growth. Adaptation plays an important role in ensuring the sustainability of food security. This research aimed to develop drought-tolerant variety of Inpari 30 (submergence tolerance variety) and Situ Bagendit through marker-assisted backcrossing-through pyramiding gene of identified QTLs for foreground selection and to explore SSRs and 6K SNPs for background selection distributed in 12 rice chromosome of drought tolerant donor (Cabacu) and recipient rice (Inpari 30 and Situ Bagendit). The foreground selection revealed that flanking SSRs of each QTLs (qRPF2.1, qGPP2.1, qSPP4.1 and Sub1) was less than 2 cM. The background selection through polymorphic survey of Rice 6K SNP primers revealed 2457 (53,3%) polymorphic SNPs on Inpari 30 vs Cabacu and 2563 (55,6%) polymorphic SNPs on Situ Bagendit vs Cabacu with the average distance about 0.74 cM/chromosome. The genotypic selection of F1 Inpari 30/Cabacu and F1 Situ Bagendit/Cabacu have already in heterozygote condition for these 4 QTLs target. These lines was continued for backcross breeding to develop BC1F1 Inpari 30/Cabacu and BC1F1 Situ Bagendit/Cabacu generation.

Super Annigeri 1 and improved JG 74: two Fusarium wilt-resistant introgression lines developed using marker-assisted backcrossing approach in chickpea (Cicer arietinum L.)

Annigeri 1 and JG 74 are elite high yielding desi cultivars of chickpea with medium maturity duration and extensively cultivated in Karnataka and Madhya Pradesh, respectively. Both cultivars, in recent years, have become susceptible to race 4 of Fusarium wilt (FW). To improve Annigeri 1 and JG 74, we introgressed a genomic region conferring resistance against FW race 4 (foc4) through marker-assisted backcrossing using WR 315 as the donor parent. For foreground selection, TA59, TA96, TR19 and TA27 markers were used at Agricultural Research Station, Kalaburagi, while GA16 and TA96 markers were used at Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur. Background selection using simple sequence repreats (SSRs) for the cross Annigeri 1 × WR 315 in BC1F1 and BC2F1 lines resulted in 76–87% and 90–95% recurrent parent genome recovery, respectively. On the other hand, 90–97% genome was recovered in BC3F1 lines in the case of cross JG 74 × WR 315. Multilocation evaluation of 10 BC2F5 lines derived from Annigeri 1 provided one superior line referred to as Super Annigeri 1 with 8% increase in yield and enhanced disease resistance over Annigeri 1. JG 74315-14, the superior line in JG 74 background, had a yield advantage of 53.5% and 25.6% over the location trial means in Pantnagar and Durgapura locations, respectively, under Initial Varietal Trial of All India Coordinated Research Project on Chickpea. These lines with enhanced resistance and high yield performance are demonstration of successful deployment of molecular breeding to develop superior lines for FW resistance in chickpea.

Introgression of Two Drought QTLs into FUNAABOR-2 Early Generation Backcross Progenies Under Drought Stress at Reproductive Stage

FUNAABOR-2 is a popular Ofada rice variety grown in a large area under rainfed upland condition across western states of Nigeria. We used the combination of phenotypic and marker-assisted selection (MAS) to improve grain yield of FUNAABOR-2 under drought stress (DS) at the reproductive stage via introgression of two drought quantitative trait loci (QTLs), qDTY12.1 and qDTY2.3. Foreground selection was carried out using peak markers RM511 and RM250, associated with qDTY12.1 and qDTY2.3, respectively, followed by recombinant selection with RM28099 and RM1261 distally flanking qDTY12.1. Furthermore, BC1F2-derived introgressed lines and their parents were evaluated under DS and non-stress (NS) conditions during the 2015–2016 dry season. Overall reduction of grain yield under DS compared to NS was recorded. Introgressed lines with qDTY12.1 and qDTY2.3 combinations showed higher yield potential compared to lines with single or no QTL under DS, indicating significant positive interactions between the two QTLs under the FUNAABOR-2 genetic background. Pyramiding of qDTY12.1 and qDTY2.3 in the FUNAABOR-2 genetic background led to higher grain yield production under DS and NS.

Breeding lines of the Indian mega-rice variety, MTU 1010, possessing protein kinase OsPSTOL (Pup1), show better root system architecture and higher yield in soils with low phosphorus

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.

Molecular breeding of ameliorating commercial pearl millet hybrid for downy mildew resistance

Downy mildew (DM) caused by Sclerospora graminicola is the most calamitous disease of pearl millet. Therefore, for introgression of DM resistance (DMR) in HHB 197 (MH-1302), an elite pearl millet hybrid, a marker-assisted breeding was undertaken by targeting three DMR loci on linkage groups (LGs) 1, 2 and 4. Breeding programme was initiated by crossing HBL 11 (DM susceptible), male parent of HHB 197 hybrid with ICMP 451 (DM-resistant) to produce true F1 plants. By conducting three rounds of backcrossing and selection, BC3F1 lines were generated. Foreground selection was employed using six polymorphic simple sequence repeat (SSR) markers of the 18 total selected markers. Four of these markers were linked to LG 1, five to LG 2 and nine to LG 4. Background selection was performed in BC3F1 generation using 33 polymorphic SSR markers of a total of 56 evenly spread SSR markers in the pearl millet genome to check recovery of recurrent parent genome. On the basis of genotypic selection (foreground as well as background) using selected SSR markers, agronomic performance in field and DM screening in greenhouse; 10 improved HBL 11 lines were selected and crossed with ICMA 97111 to produce DM-resistant HHB 197 hybrid versions. Six putatively improved HHB 197 hybrids were successfully tested in first year trials at Hisar and Bawal locations of Haryana and two selected versions with higher yield and zero DM incidence will be further tested in multilocation trials.

Marker-assisted pyramiding of two major, broad-spectrum bacterial blight resistance genes, Xa21 and Xa33 into an elite maintainer line of rice, DRR17B.

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.

Genetic and Physiological Improvement of Rice for SubmergenceTolerance

Submergence stress is a major problem in Tamil Nadu during the monsoons. Every year paddy production is greatly affected due to flash floods. A major QTL on chromosome 9, Sub1 has provided the opportunity to apply Marker Assisted Backcrossing (MAB) to develop submergence tolerant versions of rice cultivars that are widely grown in the region. Present study was at aimed at marker assisted introgression of Sub1 locus controlling submergence tolerance from FR 13A into the background of CO 43, a popularly grown rice variety in the cauvery delta region. Molecular markers that were tightly linked with Sub1, flanking Sub1, and unlinked to Sub1 were used for foreground, recombinant, and background selection, respectively, in backcrosses between a submergence tolerant donor, FR 13A and the widely grown recurrent parent, CO 43. Polymorphic markers for foreground and background selection were identified. Genotyping and phenotyping of BC1 F1 and F2 generations revealed the superiority of the plants introgressed with Sub1 locus. By the BC2 F2 and BC3 F3 generations a submergence tolerant plant was identified that possessed 100% CO 43 genome with Sub1 locus. These backcross progenies were evaluated for their tolerance against flooding. All the plants were able to survive 11 days of complete flooding.

Marker‐assisted backcross breeding for improvement of drought tolerance in bread wheat (Triticum aestivum L. em Thell)

AbstractDrought stress is presently a major productivity limiting factor in wheat. This study developed five wheat lines with inbuilt tolerance to drought stress using marker‐assisted backcross breeding (MABB) approach employing three linked quantitative trait loci (QTLs) in an initial population of 516 BC1F1 plants. The high‐yielding wheat cultivar ‘HD2733’ grown over last few years extensively in the eastern plains of India is largely sensitive to drought and is used as the recurrent parent. ‘HI1500’ released for water‐limiting conditions and carrying drought‐tolerant QTLs was used as donor parent. MABB lines were advanced using foreground and background selection, coupled with stringent phenotyping. We identified 29 lines that were homozygous for targeted QTLs in different combinations with background recovery range of 89.2%–95.4%. Further evaluation of selected lines for physiological traits and distinctness, uniformity and stability (DUS) characters under rainfed condition identified five potential varieties for national varietal evaluation programme in the zone. The report is first of its kind in implementing known QTLs for the development of drought‐tolerant wheat lines through MABB approach.

Developing Blast Disease Resistance of Jasmine Rice by Phenotypic-Genotypic Simultaneous Selection

Breeding for resistant varieties of rice is known to be the most preferable way of controlling blast disease (Pyricularia oryzae). Identification and introduction of resistance genes into elite rice lines has become possible by the use of molecular markers. KD2-1 line is an isogenic line of KDML105 carrying four resistance genes on chromosome 2, 3, 8 and 12 from IR64 variety. The objective of this research was to transfer blast disease resistant genes from KD2-1 line into RD15 variety by using phenotypic and genotypic selections by the aid of markers. In this study, the four resistance genes were transferred from KD2-1 rice line into a blast susceptible rice variety, RD15. The study resulted in the breeding of four elite rice lines with four resistance genes by phenotypic and foreground selection. The genome-wide SSR marker analysis of the lines showed more than 86.5% background genome recovery of RD15. Pathogenicity assays of the four selected lines exhibited a resistant reaction to all 13 isolates, with agronomic and yield performance, and cooking and eating quality characteristics similar to that of RD15. The phenotypic-genotypic (foreground and background) simultaneous selection strategy is very useful to introduce multiple resistance genes in rice as it is a fast and economical way for identification of anticipated recombinant lines with desired genes.

Marker Assisted Selection for Sheath Blight, Blast and Bacterial Blight Resistance in Two Popular Rice Varieties

Major biotic stresses that affects rice production are sheath blight (ShB) caused by Rhizoctonia solani Kuhn, blast disease caused by fungal pathogen Magnaporthe oryzae and bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae. To reduce the yield loss pyramiding of resistance (R) genes in an elite rice variety is the most effective method. Two high yielding rice varieties namely, ASD16 and ADT43 are extensively grown in South India. These varieties are susceptible to blast, bacterial blight and sheath blight diseases. Hence this study aims to improve these disease susceptible varieties to achieve higher yield in disease prone areas. Improved ASD16 (CB14004) harbouring BB and blast and improved ADT43 (CB14002) harbouring BB resistance genes were used in the present marker assisted backcross breeding program to introgress three sheath blight resistant QTLs (qSBR 11-1, qSBR 11-2 and qSBR 7-1). In every backcross generation, PCR-based markers (RM224, RM209 and RM336), linked with sheath blight resistance QTLs, bacterial blight resistance genes (xa5, xa13 and Xa21) and blast resistance genes (Pi54) were utilized for foreground selection. In addition, a set of forty eight (CB14002 x tetep) and forty one (CB14002) parental polymorphic SSR markers were used for background selection and backcrossing was carried out until BC3 generation. Background selection studies using polymorphic markers revealed that, an average recovery of 91.15% and the maximum of 92.68% recurrent parent genome in CB14004 x Tetep cross population. In CB14002 x Tetep an average of 90.20% and maximum of 92.70% has been recovered. These plants will be selfed to generate large number of segregating progenies to identify agronomically superior with good grain quality traits and multiple disease resistance lines in rice..

Incorporation of the novel bacterial blight resistance gene Xa38 into the genetic background of elite rice variety Improved Samba Mahsuri.

Bacterial blight (BB) in rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major global production constraint, particularly in irrigated and rain-fed lowland areas. Improved Samba Mahsuri (ISM) is an elite, high-yielding, fine-grain type, BB-resistant rice variety possessing three BB-resistant genes (Xa21, xa13 and xa5) and is highly popular in the southern parts of India. As the BB pathogen is highly dynamic and the evolution of pathogen virulence against the deployed resistance genes is common, we added a novel BB-resistant gene, Xa38, into ISM through marker-assisted backcross breeding (MABB) to increase the spectrum and durability of BB resistance. The breeding line PR 114 (Xa38) was used as the donor for Xa38, whereas ISM was used as the recurrent parent. Foreground selection was conducted using PCR-based gene-specific markers for the target genes, whereas background selection was conducted using a set of polymorphic SSR markers between the parents and backcrossing that continued until the third generation. Eighteen homozygous BC3F2 plants possessing all four BB-resistant genes in the homozygous state and with a recurrent parent genome (RPG) recovery of more than 92% were identified and advanced to the BC3F6 generation. These 18 backcross-derived lines (BDLs) exhibited very high level of resistance against multiple Xoo strains and displayed agro-morphological traits, grain qualities and yield levels similar to or better than those of the recurrent parent ISM.

DepthCut: improved depth edge estimation using multiple unreliable channels

In the context of scene understanding, a variety of methods exists to estimate different information channels from mono or stereo images, including disparity, depth, and normals. Although several advances have been reported in the recent years for these tasks, the estimated information is often imprecise particularly near depth discontinuities or creases. Studies have however shown that precisely such depth edges carry critical cues for the perception of shape, and play important roles in tasks like depth-based segmentation or foreground selection. Unfortunately, the currently extracted channels often carry conflicting signals, making it difficult for subsequent applications to effectively use them. In this paper, we focus on the problem of obtaining high-precision depth edges (i.e., depth contours and creases) by jointly analyzing such unreliable information channels. We propose DepthCut, a data-driven fusion of the channels using a convolutional neural network trained on a large dataset with known depth. The resulting depth edges can be used for segmentation, decomposing a scene into depth layers with relatively flat depth, or improving the accuracy of the depth estimate near depth edges by constraining its gradients to agree with these edges. Quantitatively, we compare against 18 variants of baselines and demonstrate that our depth edges result in an improved segmentation performance and an improved depth estimate near depth edges compared to data-agnostic channel fusion. Qualitatively, we demonstrate that the depth edges result in superior segmentation and depth orderings. (Code and datasets will be made available.)

Improvement of blast resistance of the popular high-yielding, medium slender-grain type, bacterial blight resistant rice variety, Improved Samba Mahsuri by marker-assisted breeding

Improved Samba Mahsuri (ISM) is a popular, high-yielding, bacterial blight resistant rice variety possessing medium-slender grain type. As ISM is highly susceptible to blast disease of rice, through the present study we have transferred two major blast resistance genes, Pi2 and Pi54 into the elite variety by marker-assisted backcross breeding. The two blast resistance genes were transferred to ISM through sets of backcrosses. In every backcross generation, PCR-based markers, specific for the blast resistance genes (Pi2 and Pi54) and bacterial blight resistance genes (Xa21, xa13 and xa5) were utilized for foreground selection, while a set of 144 parental polymorphic SSR markers were used for background selection and backcrossing was carried out until BC2 generation. A solitary BC2F1 plant possessing Pi2 or Pi54 along with Xa21, xa13 and xa5 and > 90% recovery of ISM genome was selected from the two sets of backcrosses were crossed and the intercross F1s (ICF1s) thus obtained were selfed to generate ICF2s. Homozygous ICF2 plants carrying all the five resistance genes were identified through markers and advanced through selfing till ICF5 generation by adopting pedigree method of selection. Three best lines at ICF5, possessing excellent resistance against bacterial blight and blast and closely resembling or superior to ISM in terms of grain quality: yield and agro-morphological traits have been identified and advanced for multi-location trials.

Marker-assisted introgression of three dominant blast resistance genes into an aromatic rice cultivar Mushk Budji

Modern high yielding rice varieties have replaced most of the traditional cultivars in recent past. Mushk Budji, is one such short grained landrace known for its aroma and exquisite quality, however, is highly susceptible to blast disease that has led to considerable decline in its area. Mushk Budji was crossed to a triple-gene donor line, DHMAS 70Q 164-1b and followed through marker-assisted foreground and background selection in first and second backcross generations that helped to incorporate blast resistance genes Pi54, Pi1 and Pita. Marker-assisted background selection was carried out using 78 SSR and STS markers that helped to reduce linkage drag around the genes Pi54, Pi1 and Pita to 2.74, 4.60 and 2.03 Mb, respectively. The three-gene lines in BC2F2:3 were genotyped using 50 K SNP chip and revealed more than 92% genome similarity to the RP. 2-D gel assay detected differentially expressing 171 protein spots among a set of backcross derived lines, of which 38 spots showing match score of 4 helped us to calculate the proteome recovery. MALDI-TOF analysis helped to detect four significant proteins that were linked to quality and disease resistance. The improved lines expressed resistance to blast under artificial and natural field conditions.

A novel aphid resistance locus in cowpea identified by combining SSR and SNP markers

AbstractThe utility of combining simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) marker genotyping was determined for genetically mapping a novel aphid (Aphis craccivora) resistance locus in cowpea breeding line SARC 1‐57‐2 and for introgressing the resistance into elite cultivars by marker‐assisted backcrossing (MABC). The locus was tagged with codominant SSR marker CP 171F/172R with a recombination fraction of 5.91% in an F2 population from ‘Apagbaala’ x SARC 1‐57‐2. A SNP‐genotyped biparental recombinant inbred line population was genotyped for CP 171F/172R, which was mapped to position 11.5 cM on linkage group (LG) 10 (physical position 30.514 Mb on chromosome Vu10). Using CP 171F/172R for foreground selection and a KASP‐SNP‐based marker panel for background selection in MABC, the resistance from SARC 1‐57‐2 was introduced into elite susceptible cultivar ‘Zaayura’. Five BC4F3 lines of improved ‘Zaayura’ that were isogenic except for the resistance locus region had phenotypes similar to SARC 1‐57‐2. This study identified a novel aphid resistance locus and demonstrated the effectiveness of integrating SSR and SNP markers for trait mapping and marker‐assisted breeding.

Improved Tapaswini having four BB resistance genes pyramided with six genes/QTLs, resistance/tolerance to biotic and abiotic stresses in rice

Rice, a major food crop, is grown in a wide range of ecological conditions and suffers significant yield losses as it is constantly exposed to a wide range of environmental and biotic stresses. The prevalence of different biotypes/strains has necessitated assembling of numerous resistance genes/QTLs into elite genotypes to confer a broader scale of resistance. The current study reports successful pyramiding of genes/QTLs that confer tolerance/resistance to submergence (Sub1), salinity (Saltol), blast (Pi2, Pi9) and gall midge (Gm1, Gm4) to supplement the four bacterial blight resistance genes (Xa 4, xa5, xa13, Xa21) present in Improved Tapaswini, an elite cultivar. The precise transfer of genes/QTLs was accomplished through effective foreground selection and suitable gene pyramids were identified. Background selection was practiced using morphological and grain quality traits to enhance the recovery of the recurrent parental genome. In the bioassays, the pyramids exhibited higher levels of resistance/ tolerance against the target stresses. The novel feature of the study was successful pyramidization and demonstration of the function of ten genes/QTLs in a new genotype. This success can stimulate several such studies to realize the full potential of molecular plant breeding as the foundation for rice improvement.

Effect of qGN4.1 QTL for Grain Number per Panicle in Genetic Backgrounds of Twelve Different Mega Varieties of Rice

BackgroundRice is a major source of food, particularly for the growing Asian population; hence, the utilization of genes for enhancing its yield potential is important for ensuring food security. Earlier, we have mapped a major quantitative trait loci (QTL) for the grain number per panicle, qGN4.1, using biparental recombinant inbred line (RIL) populations involving a new plant type Indica rice genotype Pusa 1266. Later, three independent studies have confirmed the presence of a major QTL for spikelet number by three different names (SPIKE, GPS and LSCHL4) in the same chromosomal region, and have implicated the overexpression of Nal1 gene as the causal factor for high spikelet number. However, the effect of qGN4.1 in different rice genetic backgrounds and expression levels of the underlying candidate genes is not known.ResultsHere, we report the effect of qGN4.1 QTL in the genetic backgrounds of 12 different high-yielding mega varieties of rice, introgressed by marker assisted-backcross breeding (MABB) using two QTL positive markers for foreground selection and two QTL negative flanking markers for recombinant selection together with phenotypic selection for the recovery of recipient parent genetic background. Analysis of the performance of BC2F3 plants showed a significant increase in the average number of well-filled grains per panicle in all the backgrounds, ranging from 21.6 in CSR 30-GN4.1 to 147.6 in Samba Mahsuri-GN4.1. Furthermore, qGN4.1 caused a significant increase in flag leaf width and panicle branching in most backgrounds. We identified BC3F3qGN4.1 near-isogenic lines (NILs) with 92.0–98.0% similarity to the respective recipient parent by background analysis using a 50 K rice SNP genotyping chip. Three of the NILs, namely Pusa Basmati 1121-GN4.1, Samba Mahsuri-GN4.1 and Swarna-GN4.1, showed a significant yield superiority to their recipient parents. Analysis of differential gene expression revealed that high grain number in these QTL-NILs was unlikely due to the overexpression of Nal1 gene (LOC_Os04g52479). Instead, another tightly linked gene (LOC_Os04g52590) coding for a protein kinase domain-containing protein was consistently overexpressed in the high grain number NILs.ConclusionWe have successfully introgressed the qGN4.1 QTL for high grain number per panicle into 12 different mega varieties of rice using marker-assisted backcross breeding. The advanced near-isogenic lines are promising for the development of even higher yielding versions of these high-yielding mega varieties of rice.

Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety "Pusa Basmati 1".

Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0–98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India.

Flood proofing of Ranjit, a popular variety of North-Eastern India through transfer of Sub1 rice QTL by modified marker-assisted backcross breeding

Flooding is one of the major constraints of rice production in the rainfed lowland rice ecosystem. To cope with the frequent flooding in the climate change regime, tolerant cultivars are urgently needed to protect the paddy crop from flash floods. With the help of molecular markers, a major QTL for submergence tolerance “Sub1” was introgressed into a rainfed lowland mega variety Ranjit of N.E. India, by backcrossing followed by two generations of selfing. In this modified marker-assisted backcrossing (MABC), a gene based marker Sub1BC2 and 50051 SNPs were used for foreground and background selection, respectively, in backcrosses between a Sub1 donor, Swarna-Sub1 and the recipient variety, Ranjit. The recombinant selection was skipped and background selection was deferred to BC2F2 generation. The size of the donor fragment was found to be 1.65Mb. The introgression of this small segment was possible due to large population and strict selection in segregating generations for the recurrent parent with the help of 62 DUS characters. Ranjit-Sub1, a selection in BC2F2 generation, showed background recovery of 96.54% and submergence tolerance similar to the tolerant donor parent. Yield, yield-components and grain physico-chemical properties showed successful recovery of these traits in Ranjit-Sub1, with yield potential ranging from 6.5 to 7.0 t/ha, not significantly different from the recurrent parent, Ranjit. Therefore, Ranjit-Sub1 has been recommended for Zone III for submergence stress conditions in India. The study demonstrates a rapid and highly precise strategy adopted to introgress a major QTL by BC2F2 generation into a modern rice variety using a modified MABC.

Introgression of durable blast resistance gene Pi-54 into indica rice cv. samba mahsuri, through Marker Assisted Backcross Breeding

Blast disease is one of the most significant diseases of rice, where severe infection results in more than 80% reduction in yield. It is caused by Pyricularia oryzae. New breeding strategies are essential for developing durable blast resistant varieties. The present study aimed to introgress Pi-54 gene from highly blast resistant genotype i.e. Tetep into elite rice cultivar Samba Mahsuri (BPT 5204), high yielding rice variety with good cooking quality ,but susceptible to blast disease, through Marker-Assisted Backcross Breeding programme (MABB). For foreground selection tightly linked molecular marker specific to Pi-54 gene (i.e. Pi-54MAS) which is located on chromosome 11, and it is utilized at each backcrossed generation to identify plants carrying heterozygous alleles for the targeted resistant gene. A total of 56 background markers were used to estimate the recovery of recurrent parent genome in each backcrossed generations. At BC2F2, a single plant carrying the targeted resistant gene Pi-54 with maximum recovery of recurrent parent genome (~92.80%; plant BT-8-47-22) was selected and forwarded to next generations through the selfing. Ancestry based selection procedure was employed for phenotypic disease screening and agro-morphological traits. Results confirmed that, resistance gene (Pi-54) was successfully incorporated into Samba Mahsuri. Six lines viz., BT-8-47-22-6-36, BT-8-47-22-6-55, BT-8-47-22-6-117, BT-8-47-22-6-159, BT-8-47-22-6-203 and BT-8-47-22-6-267 were identified at BC2F4 which were possessing high level of resistance to blast and agro-morphological traits similar to Samba Mahsuri. One NIL line (BT-8-47-22-6-203) was found to be better than recurrent parent Samba Mahsuri (BPT 5204) regarding grain yield per plant. This finding will be helpful in developing a blast resistant variety with highest recurrent parent genome recovery in less number of generations through the application of MABB.