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Open Access
Marker assisted development of high yielding wheat combining disease resistance and premium quality
(Punjab Agricultural University, Ludhiana, 2021) Pradeep Kumar; Sharma, Achla
Development of end product specific wheat germplasm is the comparatively newer objective in wheat breeding programme. Wheat breeding programme in our country has mainly focused on yield and resistance breeding. There has been no dedicated chapati quality breeding programme in until recent past. The present study aimed to decipher the basis of chapati quality and to develop premium quality wheat germplasm carrying high levels of stripe rust resistance and leaf rust resistance through pyramiding of Lr57/Yr40 and Yr15 rust resistance genes in premium chapati quality background. Analysis of chapati quality traits in specially constituted core set of wheat genotypes at multilocations of the state revealed that the environment in which wheat is grown has significant effect on grain quality. The major components of chapati making quality include various components such as dough handling, chapati colour, texture, flavor, taste, sweetness pliability etc. and should be given due weightage for deriving a composite chapati score. Chapati quality traits protein content (0.143), hectoliter weight (0.278), thousand grain weight (0.474), sedimentation volume (0.194), gluten index (0.260), water absorption (0.359), puffing height (0.302) were found to be positively correlated with overall chapati score. The negative correlation was found for phenol score (-0.149), water loss after baking (-0.198) and water loss after 4 hour (-0.380) with chapati score. The farinographic traits showed genotypic difference among genotypes. Identification and selection based on quick and reliable traits in segregating populations of targeted crosses is very important to develop germplasm with specific quality traits. In the segregating population, the F2 and F3 homozygous pyramided plants were identified for both the genes Lr57/Yr40 and Yr15 using KASP and SSR markers, respectively. The plants homozygous for both of the genes were further analyzed for agronomic and quality traits.
Open Access
Characterization of celery (Apium graveolens L.) genotypes for economic traits
(Punjab Agricultural University, Ludhiana, 2021) Mandeep Singh; Nara, Usha
Celery (Apium graveolens L.) is one of the important crops in Apiaceae family. It is cultivated worldwide for food as well as for use in pharmaceutics as it is an excellent source of vitamins, phenolic compounds, volatile oils and other nutrients. Identification of superior genotypes with improved biochemical and agronomic traits is essential to develop varieties for commercial cultivation. The present study focused on characterization of celery genotypes for economic traits. The performance of 20 celery genotypes over two locations during rabi 2019-20 and 2020-21 was investigated using GGE biplot analysis. The major factors influencing traits were genotypes, locations, as well as their interactions. Correlation analysis revealed a positive and significant association of seed yield with secondary branches and the number of umbels per plant. Biochemical profiling of microgreens, leaves, stalks and seeds of celery genotypes was carried out. Antioxidant activity (40.95 to 60.49%) and crude protein (28.81 to 39.94%) contents were highest in microgreens. The study revealed high content of total phenols (7.59 to 13.93 mg/g FW), total soluble sugars (20.49 to 27.77 mg/g FW), reducing sugars (10.24 to 14.83 mg/g FW), phosphorus (5.2 to 6.8 mg/g DW), iron (0.40 to 0.54 mg/g DW), copper (0.015 to 0.026 mg/g DW), ascorbic acid (0.70 to 1.77 mg/g DW), total soluble proteins (173.54 to 201.54 mg/g FW) and tocopherol (10.45 to 14.89 mg/g FW) in seeds. The concentration of total chlorophyll (1.03 to 1.54 mg/g FW), Chl a (0.80 to 1.45 mg/g FW), carotenoids (0.29 to 0.43 mg/g FW), non-reducing sugars (14.41 to 19.42 mg/g FW), and potassium (20.3 to 26.1 mg/g DW) were found highest in leaves harvested 60 DAT while that of Chl b (0.28 to 0.61 mg/g FW), zinc (0.11 to 0.19 mg/g DW), manganese (0.017 to 0.028 mg/g DW) were observed highest in leaves harvested 90 DAT. Highest contents of sodium (5.2 to 8.0 mg/g DW) and calcium (41.5 to 51.3 mg/g DW) were found in stalks harvested 60 DAT whereas crude fibre content (16.39 to 20.86%) was highest in stalks harvested 90 DAT. The study revealed the presence of total oil (17.30 to 24.05%) and essential oil (1.27 to 2.47%) in seeds of celery genotypes. Based on biochemical profiling and agronomic traits, four genotypes, namely, PAU3, PAU8, PAU16 and PAU18 were found superior in terms of seed yield and biochemical composition. Characterization of celery genotypes based on biochemical composition and yield components clustered them into four different groups.
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Molecular characterization of basmati introgression lines for spikelet per panicle QTL (qSPP2.1) AND transfer of neck blast resistance in basmati rice
(Punjab Agricultural University, Ludhiana, 2021) Navdeep Singh; Mangat, Gurjit Singh
The present day Basmati rice cultivars have lower yield potential particularly due to lower spikelet per panicle. In this study, Basmati introgression lines (BasILs) have been used which were developed by backcrossing of Punjab Basmati 3 as recurrent parent with O. longistaminata derived introgression line LIL-427 having significantly higher spikelet per panicle QTL (qSPP2.1) as donor parent. A total of 115 BasILs in BC1F5 and BC2F4 generations were evaluated in replicated trial for yield and quality traits during the kharif season 2019 at the experimental area, School of Agricultural Biotechnology, PAU, Ludhiana. Data was taken from five randomly selected plants for all the traits except plot yield and averaged. Range of variation was observed among BasILs for yield and quality traits viz; plant height, number of tillers per plant, spikelet per panicle, spikelet percentage, 1000 grain weight, grain yield, milled rice recovery (MRR), head rice recovery (HRR), grain length (GL), grain breadth (GB), length breadth ratio (L/B) and kernel length after cooking (KLAC). Analysis of variance revealed significant variation for all the traits except KLAC. A number of BasILs were identified having desirable variation for combination of different yield and quality traits. Mean spikelet per panicle in BasILs ranged from 26.7-195.4 as compared to recurrent parent Punjab Basmati 3 (81.0). Based on this variation, 46 BasILs containing 23 BasILs with significantly higher and 23 with significantly lower spikelet per panicle were selected to know the proportion of parental genome contribution with the help of 117 polymorphic SSR markers. Chromosome-wise graphical genotypes for each individual were prepared using GGT v 2.0 software which represented a clear-cut distinction between recurrent and donor parent genome per chromosome. The proportion of the recurrent parent genome ranged from 21.0-54.7 % with an average of 40.1 % for all BasILs. The proportion of the donor genome for the BC2F4 and BC1F5 progenies ranging from 37.4-75.2 % with an average of 52.5 %. The Punjab Basmati-3 accounted for an average introgression of 40.1 % in BC1F5 and 67.7 % at BC2F4 progenies. The estimated average of LIL-427 genome was 52.5 % in BC1F5 and 21.8 % in BC2F4. The 46 BasILs were further analyzed with Punjab Basmati 3 gene specific markers viz. aroma (Badh 1 & Badh 2), bacterial blight resistance (xa13 & Xa21) and amylose (RM 190). Of these, six lines were found to be positive for all the genes. Since neck blast caused by Magnaporthe oryzae remains to be the major production constraint, therefore, another experiment was undertaken with the objective to incorporate two major QTL namely qBL3 and qBL7 in the genetic background of Pusa Basmati 1121. Based on evaluation of 69 BC1F2 plants of cross Pusa Basmati 1121 X INGR15001 with SSR markers RM 141738 & RM 3484 for the presence of qBL3 and qBL7, 24 plants were found to be positive for qBL3, 5 plants for qBL7 and one plant positive for both of the QTLs. Selected BasILs containing desirable variation for yield and quality component traits and backcross progenies showing presence of neck blast resistant QTLs can be further used in breeding programme to improve yield potential of basmati rice.
Open Access
Identification of chromosomal regions associated with ear placement and related traits in maize (Zea mays L.)
(Punjab Agricultural University, Ludhiana, 2021) Tejinder Singh; Gagandeep Singh
In the present investigation, the genetic studies of ear height and its related traits were carried out by making crosses between two contrasting parents for ear height i.e, AKON40A (high ear placement) and LM23 (low ear placement) during spring 2020. The F1 hybrids were selfed to produce F2 population and backcrossed with both parents to generate BC1.1 and BC1.2 generations. Generation mean analysis was performed on all six generations i.e., P1, P2, F1, F2, BC1.1 and BC1.2 for the traits viz., plant height, ear height, no. of leaves, leaf width, node count, no. of cobs, days to anthesis, days to silking, 75% husk brown and internodal length. The significance of scaling tests for the all traits showed the presence of epistatic interactions. The genetic components revealed the presence of additive gene action, additive × additive and additive × dominance gene interaction for ear height and plant height. The variance due to environment was prevalent in both ear height and plant height. The numbers of factors governing ear height were estimated to be 236.0. Bulk segregant analysis was performed using 284 SSR markers spanning all 10 chromosomes of maize genome. Out of 146 SSR parental polymorphic markers, 9 markers were found to be polymorphic in contrasting bulks. On the basis of segregation analysis of these markers on F2 population linkage map was constructed. Three linkage groups were formed; first and third linkage group i.e., LG1 and LG3, consisted of 2 markers each, while the second linkage group consisted of 5 markers. LG1 spanned 26.9 cM on chromosome 3 while LG2 and LG3 spanned 42.1 and 6.7 cM on chromosome 6 and 7, respectively. In case of ear height, LOD score near 3 was observed on chromosome 6 between marker and phenotypic variance (R2) was 8.5, which revealed that there is a minor QTL between the SSR markers umc1979 and umc2317. On the basis of present study, recurrent selection can be utilized to improve source population for reducing ear placement by accumulating favorable alleles. Improved source population then can be utilized for inbred line development leading to maize hybrids having medium to low ear placement.
Open Access
Mapping of the Stripe rust resistance gene(s) in a nested RIL population of wheat
(Punjab Agricultural University, Ludhiana, 2021) Harjap Singh; Mavi, Gurvinder Singh
Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is one of the most devastating diseases of wheat in China and causes serious yield losses. Resistance genes are urgently needed by wheat breeding programs to combat this disease. In the present study, genetic analysis of stripe rust resistance was conducted on segregated F3 and F4 populations derived from the cross of susceptible parent PBW 621 and resistant line IC529090 and IC445316. The results showed that the resistance of stripe rust was controlled by 2 genes. In addition, GBS of the parental lines PBW 621 and IC 445316 and the corresponding bulked pools derived from homozygous resistant or susceptible F4 lines was implemented to identify single-nucleotide polymorphism (SNPs).DNA was normalized and the pool of 10 resistant and the 10 susceptible plants was made. QTSeqR package (available in R) was utilized for the bulk-segregant analysis of yellow rust using two different methods GPrime and DeltaSNP. A straightforward pipeline for analysis has been designed with the plant breeder and geneticist in mind: (i) import SNP data, (ii) filter SNPs that may complicate analysis, (iii) perform BSAs, (iv) plot results, and (v) export the data. A vignette with a stepby-step guide is available at https://github.com/bmansfeld/QTLseqr/blob/master vignettes/ QTLseqr.pdf. Nineteen (19) significant SNPs were identified by the Gprime method and 3 significant SNPs by the Delta SNP method and the 3 significant SNPs by both the Gprime and the delta SNP method. Novelty of the identified genes an be confirmed with further genetic analysis which can then be useful to broaden the narrow rust resistance spectrum in hexaploid wheat.
Open Access
Marker assisted development of high yielding wheat combining disease resistance and premium quality
(Punjab Agricultural University, Ludhiana, 2021) Pradeep Kumar; Sharma, Achla
Development of end product specific wheat germplasm is the comparatively newer objective in wheat breeding programme. Wheat breeding programme in our country has mainly focused on yield and resistance breeding. There has been no dedicated chapati quality breeding programme in until recent past. The present study aimed to decipher the basis of chapati quality and to develop premium quality wheat germplasm carrying high levels of stripe rust resistance and leaf rust resistance through pyramiding of Lr57/Yr40 and Yr15 rust resistance genes in premium chapati quality background. Analysis of chapati quality traits in specially constituted core set of wheat genotypes at multilocations of the state revealed that the environment in which wheat is grown has significant effect on grain quality. The major components of chapati making quality include various components such as dough handling, chapati colour, texture, flavor, taste, sweetness pliability etc. and should be given due weightage for deriving a composite chapati score. Chapati quality traits protein content (0.143), hectoliter weight (0.278), thousand grain weight (0.474), sedimentation volume (0.194), gluten index (0.260), water absorption (0.359), puffing height (0.302) were found to be positively correlated with overall chapati score. The negative correlation was found for phenol score (-0.149), water loss after baking (-0.198) and water loss after 4 hour (-0.380) with chapati score. The farinographic traits showed genotypic difference among genotypes. Identification and selection based on quick and reliable traits in segregating populations of targeted crosses is very important to develop germplasm with specific quality traits. In the segregating population, the F2 and F3 homozygous pyramided plants were identified for both the genes Lr57/Yr40 and Yr15 using KASP and SSR markers, respectively. The plants homozygous for both of the genes were further analyzed for agronomic and quality traits.
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Fine mapping of known QTL region for yellow mosaic disease resistance in soybean (Glycine max L. Merrill)
(Punjab Agricultural University, Ludhiana, 2021) Meghana D P; Gill, B.S.
A set of one hundred and forty-eight RILs were derived from the cross of SL958 (R) × AGS456 (S) with an aim to fine map the known QTL region for yellow mosaic disease resistance and to evaluate for grain yield and component traits were grown in the field during kharif, 2020. The experimental material was sown in randomised block design in three replications. Observations on yield and its component characters were recorded along with the YMD score. All the 148 RILs segregated in all YMD infection categories. Analysis of variance showed the presence of significant variation in RILs for all the characters recorded. Seed yield was found to have highest GCV, PCV and genetic advance. Plant height was found to be highly heritable. Seed yield recorded significant and positive correlation with number of seeds per pod, number of pods per plant, harvest index, 100-seed weight, days to 50% flowering and plant height. The results of path coefficient analysis indicated that number of pods per plant and number of seeds per pod have highest and positive direct effect on seed yield. For fine mapping of known QTL region, a total of 187 SSR markers within the known QTL region were used for parental polymorphic studies and 43 markers were found to be polymorphic. Bulk segregant analysis was conducted with 43 polymorphic markers. Out of 43 markers, 20 markers showed polymorphic on both the resistant and susceptible bulks. One major QTL explaining 58% variation for YMD resistance was observed between the markers BARCSOYSSR_06_0718 and BARCSOYSSR_06_0684 (located at a distance of 2 cM on either sides of QTL region). Gene annotation revealed that begomovirus resistance associated genes i.e; SGS3 was present in the identified QTL. The SGS3 gene along with another begomovirus resistance gene i.e; RdRp1 were amplified on genomic DNA of AGS456 and SL958. The role of differential expression of these genes in compatible and incompatible soybean-MYMV interaction is further needed to be studied. The identified markers in chromosome 6 can facilitate marker assisted selection, provide a base for cloning of YMD resistance in soybean and also help in introgressing of YMD resistance into susceptible but well adapted and popular soybean varieties.
Open Access
Genome-wide association mapping for Fe, Zn and yield traits in pigeonpea
(Punjab Agricultural University, Ludhiana, 2021) Harpreet Kaur; Inderjit Singh
In the present study, an effort was made to understand the complex nature of yield and quality traits and genome-wide association studies (GWAS) was undertaken to identify QTLs associated with traits. The analysis of variance (ANOVA) revealed significant variation among all genotypes in both the years and pooled data. Measurement of skewness and kurtosis indicated presence of duplicate and complementary gene interaction for different traits. The seed yield exhibited highly positive and significant correlation with number of primary branches per plant, number of secondary branches per plant and number of pods per plant for both the years and pooled data across two years. Path analysis identified pods per plant, number of primary and secondary branches as the major contributing traits to grain yield in both the years and pooled data. Yield per plot and pods per plant exhibited high heritability along with high genetic advance showing additive gene effect and could be considered during selection. In genotypic analysis, a total of 7366 filtered SNPs were used for genome-wide association studies through ddRAD-Seq. A total of 30 highly significant associated SNPs in 2018-19, 23 significant associated SNPs in 2019-20 and 25 significant associated SNPs in pooled data were identified through combination of two or more than two models for different traits. Most of the SNP loci were found to be environment and trait specific but few stable and consistent SNPs were identified. Some of the SNPs associated with days to maturity, yield per plot and grain iron content were observed to be consistent in 2018-19 and pooled conditions. The candidate regions were defined by the average LD decay distance or the LD block. Biological function of the identified candidate genes revealed their role in plant growth and development, organogenesis, pollen development and source-sink relationship. These genes were found to be present on chromosome 02, 03 and 09. Three polymorphic KASP markers for traits viz., grain iron content, number of primary branches and yield per plot were validated and showed that parents have homozygous alleles for the traits and alleles were found to be segregating in the F2:3 population. Promising genotypes for grain iron, grain zinc content and yield attributing traits were identified which can be used as donor parents in pigeonpea breeding programme and developed markers can be used in marker assisted selection (MAS) for identifying desirable genotypes having allele of interest.
Open Access
Identification of maize genotypes tolerant to waterlogging and their characterization using rice orthologs
(Punjab Agricultural University, Ludhiana, 2021) Thapa, Sittal; Garg, Tosh
Waterlogging, second most important abiotic constraint after drought, leads to around 25-30% of production losses each year. Identification of suitable donor lines with tolerance against waterlogging and their genetic and morphological characterization is essential to develop varieties that can overcome the ill effects posed by excess soil moisture. The present study focused on identification of maize genotypes tolerant to waterlogging and their characterization using rice orthologs. A set of 119 different genotypes belonging to different heterotic pools along with Zea mays spp parviglumis were screened at pre-emergence and seedling stage (V2) against different duration of waterlogging. In response to waterlogging all morphological parameters showed significant decline over increased duration of waterlogging. Based on selection indices, multi trait stability index (MTSI) and survival data after nine days of waterlogging, lines selected for tolerance against waterlogging are EML 153, SE 503, EML 125, AVL13119, VL 1010764, I 168, I 204, AVL13056, PML 368, LM 17, Z. mays spp parviglumis, PML 373, PML 387, EML 285, JCY 20, I 170, I 185, I 172, PML 1228, PML 243, PML 28, EML 124, LM 6, I 185 and I 192.Waterlogging tolerance coefficient (WTC) for tolerant lines lies near or above one. Broadened anthesis silking interval (>5 days) was recorded for susceptible lines, while for tolerant lines it lie within the normal range of 3-5 days. Search for ortholog genes responsible for submergence tolerance in rice revealed no significant region for SNORKEL, but significant sequence similarity for two out of three coding sequences for Sub1A. Synthesis of gene specific primers and allelic survey study showed no significant allelic variation for these genes in studied genotypes. Gene expression study revealed significantly higher fold expression of these genes in tolerant lines (up to 15 folds) during early stage of waterlogging (3 days of waterlogging) suggesting their involvement in conferring tolerance against anaerobic growth condition. Population structure analysis revealed presence of three sub-populations in our available germplasm. An average Polymorphism Information Content (PIC) value of 0.503 was obtained for SSR markers used for the genetic diversity study. Marker Trait Association (MTA) revealed two markers umc-1021 and umc-2340 to be significantly associated with both root area (-log10p of 3.91) and root volume (-log10p of 11.34).