Recurrent Parent Genome Recovery Research Articles

Pyramiding aphid resistance genes into the elite cowpea variety, Zaayura, using marker-assisted backcrossing

The cowpea aphid (Aphis cracivora) is a cosmopolitan insect pest that causes economic damage on cowpea. Although the pest persists at all the growth stages of the crop, in West Africa, aphids are the only major insect pests that farmers regularly control at the vegetative stage. Thus, deploying aphid-resistant crop varieties can reduce farmers' expenditure on insecticide. The availability of different biotypes of the pest and reports of resistance breakdown necessitates pyramiding of sources of aphid resistance to develop a more robust genotype for durable resistance. Two aphid-resistance genes, sourced from SARC-1-57-2 and IT97K-556-6, were introgressed through gene pyramiding technique into a farmers’ preferred cowpea variety, Zaayura, using marker-assisted backcrossing. A simple sequence repeat (SSR) marker, CP 171F/172R, and an allele-specific single nucleotide polymorphism (SNP) marker, 1_0912, were used for foreground selection of the SARC-1-57-2 and IT97K-556-6 aphid resistance genes, respectively. A stepwise backcross approach was used to introgress the major aphid resistance QTL (QAc-vu7.1) from IT97K-556-6 into Zaayura using the marker 1_0912 coupled with intermittent screening under artificial aphid infestation. After the fourth backcross generation, three heterozygous BC4F1 of Zaayura/TT97K-556-6 were intercrossed to Zaayura Pali to develop intercross F1 (ICF1). Three true ICF1 hybrids allowed to self to produce ICF2. Five (5) out of 48 ICF2 plants which were genotyped with the two foreground markers had the two aphid resistance genes fixed in the double homozygous dominant state. For background selection, out of 192 allele-specific markers screened, only 47 polymorphic markers were identified and used for the background analysis of the pyramided lines. The recurrent parent genome recovery ranged from 72 to 93.8 %. ICF2_Zaa/556/SARC-P6 had the highest recurrent parent genome and the least heterozygosity among the five improved lines. The five pyramided lines showed superior resistance under artificial aphid infestation as compared to the two donor parents with damage scores ranging from 2.0 to 2.3. On the field, however, there were no significant differences between the pyramided lines and their recurrent parent for all the agronomic traits measured except for grain yield. The pyramided lines do not only stand the chance of being released as new varieties but are also valuable genetic resources for other breeding programs that seek to improve cowpea for aphid resistance.

Incorporation of Photoperiod Insensitivity and High-Yield Genes into an Indigenous Rice Variety from Myanmar, Paw San Hmwe

Paw San Hmwe (PSH) is an indigenous rice variety from Myanmar with a good taste, a pleasant fragrance, and excellent elongation ability during cooking. However, its low yield potential and strong photoperiod sensitivity reduce its productivity, and it is vulnerable to climate changes during growth. To improve the photoperiod insensitivity, yield, and plant stature of PSH, the high-yield genes Grain number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP), together with the photoperiod insensitivity trait, were introgressed into PSH via marker-assisted backcross breeding and phenotype selection. For the photoperiod insensitivity trait, phenotypic selection was performed under long-day conditions during the dry season. After foreground selection of Gn1a and WFP via simple sequence repeat genotyping, genotyping-by-sequencing was conducted to validate the introgression of target genes and determine the recurrent parent genome recovery of the selected lines. The improved lines were insensitive to photoperiod, and the Gn1a and WFP introgression lines showed significantly higher numbers of primary panicle branches and spikelets per panicle than the recurrent parent, with comparative similarity in cooking and eating qualities. This study successfully improved PSH by decreasing its photoperiod sensitivity and introducing high-yield genes via marker-assisted selection. The developed lines can be used for crop rotation and double-season cropping of better-quality rice.

Genetic enhancement of reproductive stage drought tolerance in RPHR-1005R and derivative rice hybrids through marker-assisted backcross breeding in rice (Oryza sativa L.).

Drought stress is considered as one of the major production constraints in rice. RPHR-1005R is a restorer line (R-Line) with a popular, medium-slender grain type, and is the male parent of the popular Indian rice hybrid, DRR-H3. However, both the hybrid and its restorer are highly vulnerable to the drought stress, which limits the adoption of the hybrid. Therefore, the selection of the restorer line RPHR-1005R has been made with the objective of enhancing drought tolerance. In this study, we have introgressed a major QTL for grain yield under drought (qDTY 1.1) from Nagina22 through a marker-assisted backcross breeding (MABB) strategy. PCR based SSR markers linked to grain yield under drought (qDTY1.1 - RM431, RM11943), fertility restorer genes (Rf3-DRRM-Rf3-10, Rf4-RM6100) and wide compatibility (S5n allele) were deployed for foreground selection. At BC2F1, a single plant (RPHR6339-4-16-14) with target QTL in heterozygous condition and with the highest recurrent parent genome recovery (85.41%) and phenotypically like RPHR-1005R was identified and selfed to generate BC2F2. Fifty-eight homozygous lines were advanced to BC2F4 and six promising restorer lines and a hybrid combination (APMS6A/RPHR6339-4-16-14-3) were identified. In summary, the six improved restorer lines could be employed for developing heterotic hybrids possessing reproductive stage drought tolerance. The hybrid combination (APMS6A/RPHR6339-4-16-14-3) was estimated to ensure stable yields in drought-prone irrigated lowlands as well as in directly seeded aerobic and upland areas of India.

Physiological and antioxidant responses associated with Sub1 gene introgressed rice (Oryza sativa L.) lines under complete submergence.

Rice is the only crop which is well adapted to aquatic environment but, it is unable to survive if completely submerged for several weeks. Breeding rice varieties with submergence tolerance is one of the best approaches to alleviate the adverse effect of submergence which requires the introgression of Sub1 gene into elite rice varieties. Hence, the study was undertaken to introgress submergence tolerant gene into the rice variety Jaya through Marker-Assisted Backcross Breeding. Also the physiological and biochemical responses like survival percentage, underwater shoot elongation, total carbohydrate content and superoxide dismutase activity were also studied in Sub1 introgressed lines. We could develop twenty Sub1 introgressed lines with Sub1 region of 3.1-5.1mb and with 80.0- 95.3% recurrent parent genome recovery. Sub1 introgressed Jaya lines and the tolerant checks FR13A and Swarna Sub1 had lower shoot elongation under water, higher superoxide dismutase activity (about 5 times) upto 4h after de-submergence which resulted in higher survival percentage. The reduced shoot elongation of tolerant varieties reduced the utilization of stored carbohydrate. Through our research we introgressed Sub1 gene into rice variety Jaya through Marker-Assisted Backcross Breeding and could study the physiological responses under submergence by which we confirmed the presence of Sub1 gene in these lines. These lines could be field evaluated and could be released as a new variety thus helping the farmers of flood prone areas of Kerala.

Differential gene effectiveness and blast disease progression in MAS derived NILs in the background of aromatic rice landrace Mushk Budji

Mushk Budji is a premium quality scented rice landrace of Kashmir, which is highly susceptible to rice blast cause by Magnaporthe oryzae with more than 70% grain yield loss. Near-isogenic lines (NILs), namely, SKUA-27-4-40-9, SKUA-27-20-10-2 and SKUA-27-13-5-1, for the blast resistance genes, Pi54, Pi1and Pita were successfully developed in the background of Mushk Budji. Marker-assisted foreground selection was carried out using gene-based and closely linked markers viz., Pi54 MAS (Pi54), RM224 (Pi1) and YL155/87 (Pita). The background analysis was done with 90 genome-wide distributed SSR markers linked to previously tagged SNPs, which helped in estimating the recurrent parent genome (RPG) recovery in the NILs. An area under the disease progress curve (AUDPC) was drawn to test the effectiveness of the individual-resistance genes in the developed NILs. A differential reaction pattern exhibited by the individual genes helped validate the respective genes’ effectiveness under the Kashmir conditions. The Pi54 and Pita were found to be effective in conferring resistance towards M. oryzae infection in the NILs of Mushk Budji.

Evaluation of three sets of advanced backcrosses of eggplant with wild relatives from different gene pools under low N fertilization conditions.

The development of new cultivars with improved nitrogen use efficiency (NUE) is key for implementing sustainable agriculture practices. Crop wild relatives (CWRs) provide valuable genetic resources for breeding programs aimed at achieving this goal. In this study, three eggplant (Solanum melongena) accessions together with their advanced backcrosses (ABs; BC3 to BC5 generations) were evaluated for 22 morpho-agronomic, physiological, and NUE traits under low nitrogen (LN) fertilization conditions. The ABs were developed with introgressions from the wild relatives Solanum insanum, Solanum dasyphyllum, and Solanum elaeagnifolium. The AB population comprised a total of 25, 59, and 59 genotypes, respectively, with overall donor wild relative genome coverage percentages of 58.8%, 46.3%, and 99.2%. The three S. melongena recurrent parents were also evaluated under control (normal) N fertilization. Reduction of N fertilization in the parents resulted in decreased chlorophyll content-related traits, aerial biomass, stem diameter, and yield and increased NUE, nitrogen uptake efficiency (NUpE), and nitrogen utilization efficiency (NUtE). However, the decrease in yield was moderate, ranging between 62.6% and 72.6%. A high phenotypic variation was observed within each of the three sets of ABs under LN conditions, with some individuals displaying improved transgressive characteristics over the recurrent parents. Using the single primer enrichment technology 5k probes platform for high-throughput genotyping, we observed a variable but high degree of recurrent parent genome recovery in the ABs attributable to the lines recombination, allowing the successful identification of 16 quantitative trait loci (QTL). Different allelic effects were observed for the introgressed QTL alleles. Several candidate genes were identified in the QTL regions associated with plant growth, yield, fruit size, and NUE-related parameters. Our results show that eggplant materials with introgressions from CWRs can result in a dramatic impact in eggplant breeding for a more sustainable agriculture.

Gene expression of near-isogenic lines (NILs) carrying blast resistance genes Pi9 and Pi54 in the background of rice cultivar Mushk Budji.

Kashmir valley, India is a homeland to rice landraces like Zag, Nunbeoul, Qadirbeigh, Kawkadur, Kamad, Mushk Budji, etc., generally characterized by short grains, aroma, earliness and cold tolerance. Mushk Budji is a commercially important speciality rice known for its taste and aroma, nonetheless, is extremely vulnerable to blast disease. Through the use of the marker-assisted backcrossing (MABC) approach, a set of 24 Near-isogenic lines (NILs) was created, and the lines with the highest background genome recovery were chosen. The expression analysis was carried out for the component genes and other eight pathway genes related to blast resistance. The major blast resistance genes Pi9 (from IRBL-9W) and Pi54 (from DHMAS 70Q 164-1b) were incorporated following simultaneous-but-step-wise MABC. The NILs harbouring genes Pi9 + Pi54, Pi9 and Pi54 expressed resistance to isolate (Mo-nwi-kash-32) under controlled and natural field conditions. The loci controlling ETI (effector triggered immunity) included the gene Pi9 and showed 61.18 and 60.27 fold change in relative gene expression in Pi54 + Pi9 and Pi9 carrying NILs against RP Mushk Budji. Pi54 was up regulated and showed 41 and 21 fold change in relative gene expression for NIL-Pi54 + Pi9 and NIL-Pi54, respectively. Among the pathway genes, LOC_Os01g60600 (WRKY 108) recorded 8 and 7.5 fold up regulation in Pi9 and Pi54 NILs. The NILs showed recurrent parent genome recovery (RPG) per cent of 81.67 to 92.54 and were on par in performance to recurrent parent Mushk Budji. The lines were utilized to study the expression of the loci controlling WRKYs, peroxidases and chitinases that confer overall ETI response.

Provitamin A, lysine and tryptophan enrichment in shrunken2-based sweet corn genotypes through genomics-assisted breeding for crtRB1 and opaque2 genes

Malnutrition affects large section of population worldwide. VitaminA and protein deficiencies have emerged as the major global health-issue. Traditional shrunken2 (sh2)-based sweet corn is deficient in provitaminA (proA), lysine and tryptophan. Natural variant of β-carotene hydroxylase1 (crtRB1) and opaque2 (o2) enhances proA, lysine and tryptophan in maize. So far, no sweet corn hybrid rich in these nutrients has been released elsewhere. Development of biofortified sweet corn hybrids would help in providing the balanced nutrition. We targeted three sh2-based sweet corn inbreds (SWT-19, SWT-20 and SWT-21) for introgression of mutant crtRB1 and o2 genes using molecular breeding. The gene-based 3'TE-InDel and simple sequence repeat(SSR) (umc1066) markers specific to crtRB1 and o2, respectively were utilized in foreground selection in BC1F1, BC2F1 and BC2F2. Segregation distortion was observed for crtRB1 and o2 genes in majority of populations. Background selection using 91-100 SSRs revealed recovery of recurrent parent genome (RPG) up to 96%. The introgressed progenies possessed significantly higher proA (13.56µg/g) as compared to the original versions (proA: 2.70µg/g). Further, the introgressed progenies had accumulated moderately higher level of lysine (0.336%) and tryptophan (0.082%) over original versions (lysine: 0.154% and tryptophan: 0.038%). Kernel sweetness among introgressed progenies (17.3%) was comparable to original sweet corn (17.4%). The introgressed inbreds exhibited higher resemblance with their recurrent parents for yield and morphological characters. These newly developed biofortified sweet corn genotypes hold immense promise to alleviate malnutrition.

Blast resistance (Pi54) introgression in temperate rice (Oryza sativa L.) K343 using marker assisted backcrossing

In hill rice ecologies, Magnaporthe oryzae causes rice blasts and a significant biotic constraint. The study was aimed to develop rice blast-resistant lines/varieties through marker-assisted selection (MAS) by using the Pi54 gene, which provides resistance against the most prominent blast fungus isolate (PLP-1). The blast resistance gene Pi54 from the indica rice genotype DHMAS has been inserted into the genetic makeup of the temperate rice variety K343 in the current study. Three SSR markers (TRS26, TRS33, and RM206) are closely linked to the Pi54 locus used in this study. Marker RM206, located 0.7cM from the Pi54 gene, distinguished between donor and recipient alleles and co-segregated with the target gene. Thus, RM206 is used for Pi54 gene foreground selection. Sixty-one plants have the homozygous allele for the Pi54 in BC1F2, accounting for roughly 50% of the homozygous population. Polymorphic genome-wide SSR assessment of the BC1F2 genetic stock (K343*2/DHMAS) revealed recurrent parent genome (RPG) recovery above 75% in 4 plants. Therefore, M. oryzae race PLP-1, the dominant race used in this study, showed high resistance to the resistant response after inoculation.

Marker Assisted Introgression of Resistance Genes and Phenotypic Evaluation Enabled Identification of Durable and Broad-Spectrum Blast Resistance in Elite Rice Cultivar, CO 51

Across the globe, rice cultivation is seriously affected by blast disease, caused by Magnaporthe oryzae. This disease has caused heavy yield loss to farmers over the past few years. In this background, the most affordable and eco-friendly strategy is to introgress blast-resistant genes from donors into elite rice cultivars. However, it is not only challenging to evolve such resistance lines using conventional breeding approaches, but also a time-consuming process. Therefore, the marker-assisted introduction of resistance genes has been proposed as a rapid strategy to develop durable and broad-spectrum resistance in rice cultivars. The current study highlights the successful introgression of a blast resistance gene, i.e., Pi9, into CO 51, an elite rice cultivar which already has another resistance gene named Pi54. The presence of two blast resistance genes in the advanced backcross breeding materials (BC2F2:3) was confirmed in this study through a foreground selection method using functional markers such as NBS4 and Pi54MAS. The selected positive introgressed lines were further genotyped for background selection with 55 SSR markers that are specific to CO 51. Consequently, both Pi9 as well as Pi54 pyramided lines, with 82.7% to 88.1% of the recurrent parent genome recovery, were identified and the selected lines were evaluated under hotspot. The analysis outcomes found that both the lines possessed a high level of resistance against blast disease during the seedling stage itself. In addition to this, it was also noticed that the advanced breeding rice lines that carry Pi9 + Pi54 were effective in nature and exhibited a higher degree of resistance against blast disease compared to the lines that were introgressed with a single blast resistance gene. Thus, the current study demonstrates a rapid and a successful introgression and pyramiding of two blast resistance genes, with the help of markers, into a susceptible yet high-yielding elite rice cultivar within a short period of time. Those gene pyramided rice lines can be employed as donors to introgress the blast-resistant genes in other popular susceptible cultivars.

Backcrossing with Marker Assistance to Introduce Broad-Spectrum Bacterial Leaf Blight Resistance in the Malaysian Elite Variety MR297

A significant part of marker-assisted backcross breeding (MABB) is recurrent parent genome recovery (RPGR). The purpose of this study was to introduce MABB-mediated resistance genes against numerous bacterial leaf blight (BLB) pathogens. Here, we examine the introgression of four Xoo resistance genes to the high-yielding Malaysian MR297 lineage Xa21, xa13, xa5, and Xa4 from the IRBB60 lineage. To accomplish both foreground and background selection, we employed polymorphic functional linked markers to target genes and simple sequence repeat (SSR) markers. We used 83 of the 475 authorized polymorphic microsatellite markers to determine the proportion of RPGR in the chosen lines. According to the data, the RPGR at BC1F1, BC2F1, and BC2F2 are 81.94, 92.30, and 95.04%, respectively. Incorporating the four BLB resistance genes into the newly created lines would result in long-lasting and comprehensive protection against BLB. Therefore, a resistant gene may be introduced into a population more quickly with MABB than through conventional breeding. All ten lines tested showed a significant level of resistance to BLB, with three lines displaying very high levels of resistance. Consequently, it was recommended that new lines should be used to produce commercially viable rice varieties.

Marker-Assisted Introgression of the Salinity Tolerance Locus Saltol in Temperate Japonica Rice

BackgroundRice is one of the most salt sensitive crops at seedling, early vegetative and reproductive stages. Varieties with salinity tolerance at seedling stage promote an efficient growth at early stages in salt affected soils, leading to healthy vegetative growth that protects crop yield. Saltol major QTL confers capacity to young rice plants growing under salt condition by maintaining a low Na+/K+ molar ratio in the shoots.ResultsMarker-assisted backcross (MABC) procedure was adopted to transfer Saltol locus conferring salt tolerance at seedling stage from donor indica IR64-Saltol to two temperate japonica varieties, Vialone Nano and Onice. Forward and background selections were accomplished using polymorphic KASP markers and a final evaluation of genetic background recovery of the selected lines was conducted using 15,580 SNP markers obtained from Genotyping by Sequencing. Three MABC generations followed by two selfing, allowed the identification of introgression lines achieving a recovery of the recurrent parent (RP) genome up to 100% (based on KASP markers) or 98.97% (based on GBS). Lines with highest RP genome recovery (RPGR) were evaluated for agronomical-phenological traits in field under non-salinized conditions. VN1, VN4, O1 lines were selected considering the agronomic evaluations and the RPGR% results as the most interesting for commercial exploitation. A physiological characterization was conducted by evaluating salt tolerance under hydroponic conditions. The selected lines showed lower standard evaluation system (SES) scores: 62% of VN4, and 57% of O1 plants reaching SES 3 or SES 5 respectively, while only 40% of Vialone Nano and 25% of Onice plants recorded scores from 3 to 5, respectively. VN1, VN4 and O1 showed a reduced electrolyte leakage values, and limited negative effects on relative water content and shoot/root fresh weight ratio.ConclusionThe Saltol locus was successfully transferred to two elite varieties by MABC in a time frame of three years. The application of background selection until BC3F3 allowed the selection of lines with a RPGR up to 98.97%. Physiological evaluations for the selected lines indicate an improved salinity tolerance at seedling stage. The results supported the effectiveness of the Saltol locus in temperate japonica and of the MABC procedure for recovering of the RP favorable traits.

Ugradnja Ga1-S gena u roditeljske linije hibrida kukuruza belog zrna pomoću molekularnih markera

Maize Research Institute Zemun Polje has a marker-assisted backcross breeding (MABB) program aimed to incorporate the strong allele of incompatibility gene Ga1 into parental components of the hybrids with specific traits (white kernel). The main objective of this research was marker-assisted development of the white maize hybrid's parental lines with complete cross-incompatibility to foreign pollens. Ga1-S-tightly-linked molecular markers successfully identified heterozygous plants with a percentage of approximately 50% after all three backcrossings. Regarding the background selection, 69% of progenies had recurrent parent's genome (RPG) above the theoretical value for BC3 generation. Also, a few individuals even had 99%, the value theoretically achieved in the BC6 generation, showing that MABB made a genetic gain in RPG recovery. Foreground selection in this generation aimed to identify homozygous dominant individuals. Out of 264 BC3 F2 plants, 70 (26.5%) were dominant homozygotes, which is in accordance with the expected Mendelian ratio. Progenies of the BC3 F2 homozygous dominant plants were planted alternatively with yellow-kernel maize of the same maturity to check cross-incompatibility. Unfortunately, none of the dominant progenies had a 100% white kernel, most likely due to the presence of modifier genes that increase/decrease the effectiveness of pollen exclusion or that, alternatively, modifiers are lost during the backcrossing. It could be expected that successfully employed functional markers (developed from the sequence polymorphisms present within a functional gene(s) associated with phenotypic trait variations) would outbalance the noted impediments and enhance MABB efficiency to transfer the desired gene(s) controlling simple or complex trait(s) into cultivated varieties.

The resurrection of sweet corn inbred SC11-2 using marker aided breeding for β-carotene

Sweet corn has dominated the urban market due to its sweetness, tenderness, and ease of digestibility. It's import and export values have dramatically increased during the past 10 years as a fresh, processed, and preserved commodity. However, the commercially available sweet corns are deficient in β-carotene. In our study, we introgressed the favorable allele of crtRB1 (responsible for high β-carotene) into the recurrent sweet corn inbred SC11-2 from maize donor parent UMI1230β1+ to develop the β-carotene-rich sweet corn genotype by marker aided breeding. The crtRB1 3′TE InDel marker was utilized for foreground selection of favorable genotype. A total of 103 polymorphic SSR markers were employed for background selection, resulting in a 96% recovery of recurrent parent genome (RPG). We recorded high β-carotene content (9.878–10.645 μg/g) in the introgressed lines compared to the recurrent parent, SC11-2 (0.989 μg/g). The sugar content ranged from 18 to 19.10% and was on par with the recurrent parent (20.40%). These biofortified inbreds can be used as a donor in maize breeding programs to develop sweet corn genotypes with high β-carotene content.

Assessing the Effect of a Major Quantitative Locus for Phosphorus Uptake (Pup1) in Rice (O. sativa L.) Grown under a Temperate Region

Water and phosphorus (P) fertilizer are two of the most critical inputs in rice cultivation. Irrigation and chemical fertilizers are becoming limiting factors under climate change and urbanization, which is leading to significant losses in yield. The Pup1 quantitative trait locus (QTL) confers tolerance to P starvation through enhanced early-stage root vigor and P uptake in indica rice grown in the tropics. Whether the QTL works in temperate rice genetic backgrounds grown in temperate regions remains to be elucidated. To address this question, we introgressed the Pup1 QTL into three temperate rice varieties—MS11, TR22183, and Dasanbyeo—using marker-assisted backcrossing and high-density genotyping. The selected lines all harbored the full Pup1 QTL with recurrent parent genome recovery rates ranging from 66.5% to 99.8%. Under the rainfed and P non-supplied conditions, Pup1 introgression lines did not show clear advantages over the recurrent parents in terms of vegetative growth and grain yield per plant, but exhibited enhanced yield responses to P application, except in Dasanbyeo, which a temperate rice that is genetically similar to indica. Our results suggest that Pup1 confers enhanced P uptake in temperate rice and that the efficacy of Pup1 might depend on the subspecific genomic background of the rice, whether it is japonica or indica.

Molecular Breeding of Water-Saving and Drought-Resistant Rice for Blast and Bacterial Blight Resistance.

Rice production is often affected by biotic and abiotic stressors. The breeding of resistant cultivars is a cost-cutting and environmentally friendly strategy to maintain a sustainable high production level. An elite water-saving and drought-resistant rice (WDR), Hanhui3, is susceptible to blast and bacterial blight (BB). This study was conducted to introgress three resistance genes (Pi2, xa5, and Xa23) for blast and BB into Hanhui3, using marker-assisted selection (MAS) for the foreground selection and a whole-genome single-nucleotide polymorphism (SNP) array for the background selection. As revealed by the whole-genome SNP array, the recurrent parent genome (RPG) recovery of the improved NIL was 94.2%. The resistance levels to blast and BB of the improved NIL and its derived hybrids were higher than that of the controls. In addition, the improved NIL and its derived hybrids retained the desired agronomic traits from Hanhui3, such as yield. The improved NIL could be useful to enhance resistance against biotic stressors and produce stable grain yields in Oryza sativa subspecies indica rice breeding programs.

Genetic improvement of traditional Basmati rice Ranbir Basmati for semi-dwarfism and blast resistance through molecular breeding

The traditional Basmati rices grown in north-western foothills of Himalayas in India are known world-wide for their exquisite aroma and exceptional eating and cooking qualities. These varieties are tall and suffer heavy losses due to their susceptibility to lodging as well as blast disease. In present study, we improved a popular traditional Basmati rice variety ‘Ranbir Basmati’ for semi-dwarfism and resistance to blast by incorporating the semi-dwarfing gene, sd1 and two blast resistance genes, Pi9 and Pi54 through marker-assisted backcross breeding. Combining marker-assisted background selection with stringent phenotypic selection for aroma and seed quality traits during backcrossing enabled faster recovery of recurrent parent genome and reconstitution of the genomic regions associated with Basmati quality traits in the gene pyramided lines. All pyramided lines were significantly short statured with a reduction of 23.46 to 40.26 cm in height, as compared to recurrent parent, with many of them exhibiting higher grain yield and superior quality attributes than Ranbir Basmati. The yield superiority of the pyramided lines primarily resulted from the improvement in panicle number and semi-dwarf stature conferred by sd1 gene. The gene pyramided lines showed complete resistance to five highly virulent blast races that collectively showed compatibility with 16 different resistance genes, suggesting the broad-spectrum resistance in these lines. The semi-dwarf, high yielding and blast resistant lines generated herein are potential candidates for release as cultivars for overcoming losses in Ranbir Basmati due to lodging and blast disease.

Relationship between Acylsugars and Leaf Trichomes: Mediators of Pest Resistance in Tomato.

Simple SummarySeveral pests have the potential to cause major damage to tomatoes. The two-spotted spider mite and whitefly are examples of pests that attack tomato crops. Management of these pests involves several techniques; the use of chemical products is the most adopted strategy. However, growing resistant genotypes is a promising strategy in pest management, reducing the use of chemical products. In this work, we sought to identify genotypes more resistant to the mite and whitefly using advanced populations of tomato (F2BC3) obtained from the cross between S. lycopersicum “Redenção” and S. pennellii, accession LA-716. Results indicated a greater resistance in the genotypes with high levels of acylsugars, a chemical compound commonly found in S. pennellii tomatoes. Consequently, genotypes with increased levels of acylsugar can be used in breeding programs for pest resistance.Tomato plants are highly susceptible to pests. Among the control methods, genetic improvement with introgression of resistance genes from wild accessions into commercial tomato lines is the best alternative for an integrated pest management (IPM). Thus, the objective of this study was to select tomato genotypes in advanced populations (F2BC3), with higher levels of acylsugar content, greater recurrent parent genome recovery, and resistance to Tetranychus urticae and Bemisia tabaci inherited from Solanum pennellii. For pest resistance, bioassays were assessed: nine high-acylsugar genotypes, four low-acylsugar genotypes, and the parents, Solanum lycopersicum or ‘Redenção’, and Solanum pennellii LA-716. Glandular and non-glandular trichomes were quantified. A negative correlation was measured between acylsugar content in the leaflets and pest behavior. Pest resistance was found in the selected F2BC3 genotypes with high-acylsugar content, indicating that this allelochemical was efficient in controlling the arthropod pests.

DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials

BackgroundImproved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL, Saltol, associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6–11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the Saltol QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29).ResultsForeground selection was carried out at each generation using five Saltol-specific markers and three bacterial blight resistance genes, Xa21, xa13 and xa5. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC3F2 generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC3F4 generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for Saltol and OsSKC1 (Shoot K+Concentration 1).ConclusionDRR Dhan 58, possessing Saltol and three bacterial blight resistance genes (Xa21, xa13 and xa5) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.

Development of High Yielding Fusarium Wilt Resistant Cultivar by Pyramiding of "Genes" Through Marker-Assisted Backcrossing in Chickpea (Cicer arietinum L.).

Pusa 391, a mega desi chickpea variety with medium maturity duration is extensively cultivated in the Central Zone of India. Of late, this variety has become susceptible to Fusarium wilt (FW), which has drastic impact on its yield. Presence of variability in the wilt causing pathogen, Fusarium oxysporum f.sp. ciceri (foc) across geographical locations necessitates the role of pyramiding for FW resistance for different races (foc 1,2,3,4 and 5). Subsequently, the introgression lines developed in Pusa 391 genetic background were subjected to foreground selection using three SSR markers (GA16, TA 27 and TA 96) while 48 SSR markers uniformly distributed on all chromosomes, were used for background selection to observe the recovery of recurrent parent genome (RPG). BC1F1 lines with 75–85% RPG recovery were used to generate BC2F1. The plants that showed more than 90% RPG recovery in BC2F1 were used for generating BC3F1. The plants that showed more than 96% RPG recovery were selected and selfed to generate BC3F3. Multi-location evaluation of advanced introgression lines (BC2F3) in six locations for grain yield (kg/ha), days to fifty percent flowering, days to maturity, 100 seed weight and disease incidence was done. In case of disease incidence, the genotype IL1 (BGM 20211) was highly resistant to FW in Junagarh, Indore, New Delhi, Badnapur and moderately resistant at Sehore and Nandyal. GGE biplot analysis revealed that IL1(BGM20211) was the most stable genotype at Junagadh, Sehore and Nandyal. GGE biplot analysis revealed that IL1(BGM 20211) and IL4(BGM 20212) were the top performers in yield and highly stable across six environments and were nominated for Advanced Varietal Trials (AVT) of AICRP (All India Coordinated Research Project on Chickpea) in 2018–19. BGM20211 and BGM 20212 recorded 29 and 28.5% average yield gain over the recurrent parent Pusa 391, in the AVT-1 and AVT-2 over five environments. Thus, BGM20211 was identified for release and notified as Pusa Manav/Pusa Chickpea 20211 for Madhya Pradesh, Gujarat and Maharashtra, Southern Rajasthan, Bundhelkhand region of Uttar Pradesh states 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 (Gazette notification number S.O.500 (E) dt. 29-1-2021).Such pyramided lines give resilience to multiple races of fusarium wilt with added yield advantage.