N. S. Bains

Development of high yielding IR64 × Oryza rufipogon (Griff.) introgression lines and identification of introgressed alien chromosome segments using SSR markers

Modern rice varieties that ushered in the green revolution brought about dramatic increase in rice production worldwide but at the cost of genetic diversity at the farmers’ fields. The wild species germplasm can be used for broadening the genetic base and improving productivity. Mining of alleles at productivity QTL from related wild species under simultaneous backcrossing and evaluation, accompanied by molecular marker analysis has emerged as an effective plant breeding strategy for utilization of wild species germplasm. In the present study, a limited backcross strategy was used to introgress QTL associated with yield and yield components from Oryza rufipogon (acc. IRGC 105491) to cultivated rice, O. sativa cv IR64. A set of 12 BC2F6 progenies, selected from among more than 100 BC2F5 progenies were evaluated for yield and yield components. For plant height, days to 50% flowering and tillers/plant, the introgression lines did not show any significant change compared to the recurrent parent IR64. For yield, 9 of the 12 introgression lines showed significantly higher yield (19–38%) than the recurrent parent IR64. Four of these lines originating from a common lineage showed higher yield due to increase in grain weight and another three also from a common lineage showed yield increase due to increase in grain number per panicle. For analyzing the introgression at molecular level all the 12 lines were analyzed for 259 polymorphic SSR markers. Of the total 259 SSR markers analyzed, only 18 (7.0%) showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6 and 11. Graphical genotypes have been prepared for each line and association between the introgression regions and the traits that increased yield is reported. Based on marker trait association it appears that some of the QTL are stable across the environments and genetic backgrounds and can be exploited universally.

A comparison of cytoplasmic and chemically-induced male sterility systems for hybrid seed production in wheat (Triticum aestivum L.)

A comparison of two male sterility systems was carried out in wheat for hybrid seed production and hybrid performance. Seventeen hybrid combinations based on Triticum timopheevi cytoplasm were compared with their genetically equivalent CHA-facilitated combinations. The same set of restorer lines was used as parents in CMS- and CHA-based hybrids to maintain genetic equivalence. In the first experiment aimed at study of female line behavior and crossed seed production, the CHA treated lines showed significantly shorter heights whereas CMS lines were similar to the control. The two systems were equally effective in sterilizing rate. The outcrossing percentage of the CMS lines was almost twice that of the CHA treated lines. Thousand-grain weight of the crossed seeds on CMS lines was greater than on the CHA treated lines and control. On average, the germination percentage of seeds on CMS lines was double that of the CHA treated lines and the percentage of effective outcrossed seeds in CMS lines was 3 times more than that from CHA treated lines. The second experiment was conducted to examine the yield performance of the hybrids derived from the two systems of male sterility. A total of 40 entries including 20 hybrids and 20 parents were evaluated in the experiment. The mean grain yield of the CMS-based hybrids was greater than that of the CHA-based hybrids,the B and R lines. All the CMS-based hybrids showed significantly higher grain yields than their better parents whereas all the CHA-based hybrids, except two,showed no significant yield increases over their better parents. Possible reasons for differences in CMS- and CHA-based hybrid performance are discussed.

Multi-trait and multi-environment QTL analyses for resistance to wheat diseases

Background Stripe rust, leaf rust, tan spot, and Karnal bunt are economically significant diseases impacting wheat production. The objectives of this study were to identify quantitative trait loci for resistance to these diseases in a recombinant inbred line (RIL) from a cross HD29/WH542, and to evaluate the evidence for the presence loci on chromosome region conferring multiple disease resistance. Methodology/Principal Findings The RIL population was evaluated for four diseases and genotyped with DNA markers. Multi-trait (MT) analysis revealed thirteen QTLs on nine chromosomes, significantly associated with resistance. Phenotypic variation explained by all significant QTLs for KB, TS, Yr, Lr diseases were 57%, 55%, 38% and 22%, respectively. Marginal trait analysis identified the most significant QTLs for resistance to KB on chromosomes 1BS, 2DS, 3BS, 4BL, 5BL, and 5DL. Chromosomes 3AS and 4BL showed significant association with TS resistance. Significant QTLs for Yr resistance were identified on chromosomes 2AS, 4BL and 5BL, while Lr was significant on 6DS. MT analysis revealed that all the QTLs except 3BL significantly reduce KB and was contributed from parent HD29 while all resistant QTLs for TS except on chromosomes 2DS.1, 2DS.2 and 3BL came from WH542. Five resistant QTLs for Yr and six for Lr were contributed from parents WH542 and HD29 respectively. Chromosome region on 4BL showed significant association to KB, TS, and Yr in the population. The multi environment analysis for KB identified three putative QTLs of which two new QTLs, mapped on chromosomes 3BS and 5DL explained 10 and 20% of the phenotypic variation, respectively. Conclusions/Significance This study revealed that MT analysis is an effective tool for detection of multi-trait QTLs for disease resistance. This approach is a more effective and practical than individual QTL mapping analyses. MT analysis identified RILs that combine resistance to multiple diseases from parents WH542 and/or HD29.

Unlocking the genetic diversity of Creole wheats.

Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement.

Putrescine modulates antioxidant defense response in wheat under high temperature stress

Effects of putrescine (Put) on responses of wheat (Triticum aestivum) seedlings or detached tillers at mid-milky stage to high temperature (HT) stress were investigated. The heat tolerant cv. PBW 343 exhibited higher content of antioxidants and activities of antioxidative enzymes, while lower content of lipid peroxides as compared to the heat-sensitive cv. HD 2329. HT elevated peroxidase (POX) and superoxide dismutase (SOD) activities, while diamine oxidase (DAO) and polyamine oxidase (PAO) activities were reduced in roots, shoots and developing grains. Application of Put under HT further enhanced POX and SOD activities along with increased content of ascorbate and tocophereol in grains. Invariably POX and SOD revealed higher activities in roots while CAT, DAO and PAO activities were higher in shoots. The content of lipid peroxides was increased in roots and shoots of HT stressed seedlings but less in Put-treated cv. PBW 343.

Stimulation of antioxidative enzymes and polyamines during stripe rust disease of wheat

Content of polyamines and activities of antioxidative enzymes in response to stripe rust disease caused by Puccinia striiformis have been studied in two wheat (Triticum aestivum L.) cultivars PBW 343 (resistant) and HD 2329 (susceptible). Various infection stages ranging from traces to 100 % were collected. Infection leads to stimulation of peroxidase (POD), superoxide dismutase (SOD), catalase, diamine oxidase and polyamine oxidase activities along with increase in putrescine, spermidine and spermine content while ascorbate, tocopherol and chlorophyll content decreased in HD 2329 and no visible symptoms appeared in PBW 343. Histochemical localization pattern of POD and SOD activities revealed correlation with lignin deposition in cell walls.

Additive genes at nine loci govern Karnal bunt resistance in a set of common wheat cultivars

The genetics of Karnal bunt (KB) resistance were studied in populations derived from crosses of four resistant stocks (HD 29, W 485, ALDAN ‘S’/IAS 58, H 567.71/ 3*PAR) and a highly susceptible cultivar, WH 542. The plant materials screened for KB response consisted of F2, BC1 and RILs from all ‘Resistant’בSusceptible’ crosses and RILs from the six possible ‘Resistant’ × ‘Resistant’ crosses as well as the parents and F1s. The screening was performed under optimal conditions for disease development with a mixture of isolates from North Western Plains of India using the widely followed syringe method of inoculation. The KB scores of the F1 from the four ‘Resistant’ × ‘Susceptible’ crosses indicated partial dominance of resistance. Genetic analysis revealed that HD 29, W485 and ALDAN ‘S’/IAS 58 each carried two resistance genes whereas 3 genes were indicated in H 567.71/3*PAR. The six ‘Resistant × Resistant’ RIL sets showed that the genes in the four resistant stocks were different and that there may be as many as nine genes governing KB resistance in the four parents.

Yield-Enhancing Heterotic QTL Transferred from Wild Species to Cultivated Rice Oryza sativa L

Utilization of “hidden genes” from wild species has emerged as a novel option for enrichment of genetic diversity for productivity traits. In rice we have generated more than 2000 lines having introgression from ‘A’ genome-donor wild species of rice in the genetic background of popular varieties PR114 and Pusa44 were developed. Out of these, based on agronomic acceptability, 318 lines were used for developing rice hybrids to assess the effect of introgressions in heterozygous state. These introgression lines and their recurrent parents, possessing fertility restoration ability for wild abortive (WA) cytoplasm, were crossed with cytoplasmic male sterile (CMS) line PMS17A to develop hybrids. Hybrids developed from recurrent parents were used as checks to compare the performance of 318 hybrids developed by hybridizing alien introgression lines with PMS17A. Seventeen hybrids expressed a significant increase in yield and its component traits over check hybrids. These 17 hybrids were re-evaluated in large-size replicated plots. Of these, four hybrids, viz., ILH299, ILH326, ILH867 and ILH901, having introgressions from O. rufipogon and two hybrids (ILH921 and ILH951) having introgressions from O. nivara showed significant heterosis over parental introgression line, recurrent parents and check hybrids for grain yield-related traits. Alien introgressions were detected in the lines taken as male parents for developing six superior hybrids, using a set of 100 polymorphic simple sequence repeat (SSR) markers. Percent introgression showed a range of 2.24 from in O. nivara to 7.66 from O. rufipogon. The introgressed regions and their putative association with yield components in hybrids is reported and discussed.

MOLECULAR MAPPING OF LEAF AND STRIPE RUST RESISTANCE GENES IN T. MONOCOCCUM AND THEIR TRANSFER TO HEXAPLOID WHEAT

Wheat as a crop has benefited immensely from genetic improvement programmes but wheat production is still being challenged constantly by several diseases; among them, rusts are the most prominent. Leaf rust is the most widely distributed desease of wheat despite the fact that major emphasis has been made to develop rust resistant varieties. Deployment of major genes has often turned out to be non-durable and in India most of the genes identified from cultivated germplasm are not effective against the prevalent pathotypes of leaf rust. A spring type Triticum monococcum (acc. 14087) has maintained a high level of resistance to Indian isolates of leaf and stripe rust. Genetic studies using a set of 125 recombinant inbred lines (RILs), developed from a cross T. monococcum (acc. 14087)/T. boeoticum (acc. 5088) revealed that both T. monococcum and T. boeoticum have one APR gene that confers resistance to stripe rust and one seedling and one adult plant resistance gene for leaf rust. A genome linkage map with more than 150 markers, including RFLPs, SSRs and bin mapped ESTs, has been generated using the RIL population. QTL analysis revealed the presence of leaf and stripe rust resistance genes on chromosome 2A. Attempts were made to transfer both leaf and stripe rust resistance genes from T. monococcum to hexaploid wheat using T. durum cv N59 as a bridging species. Screening of F1 and backcross generations revealed that B genome of T. durum suppresses resistance of T. monococcum. With subsequent backcrosses one seedling and one APR gene for leaf rust and one APR gene for stripe rust resistance have been transferred from T. monococcum to bread wheat cv. WL711 and one APR gene for leaf rust has been transferred in PBW343 background. Chromosome number of the resistant plants varied from 39–kern0.5pt41. The leaf and stripe rust resistant plants are being analyzed with SSR markers that were found to be associated with leaf and stripe rust resistance genes based on QTL mapping in the RIL population

Genome-Wide Association Study of Grain Architecture in Wild Wheat Aegilops tauschii

Aegilops tauschii, the D-genome progenitor of Triticum aestivum, encompasses huge diversity for various traits of potential economic importance such as yield, biotic and abiotic stress tolerance, quality and nutrition. In the present study, variation for grain size in Ae. tauschii germplasm was studied and its genetic basis dissected using genome-wide association study (GWAS). Grain length, width, and weight evaluated in 177 Ae. tauschii accessions over 3 years showed near normal distribution with 1.74-, 1.75-, and 2.82-fold variation, respectively. These lines were genetically characterized using genotyping-by-sequencing (GBS) protocol that produced 11,489 single nucleotide polymorphic (SNP) markers. Genetic diversity analysis revealed the presence of two distinct subgroups (designated as lineage 1 and 2) in Ae. tauschii. Based on GBS markers, the genetic similarity was calculated between the accessions and GWAS was conducted using 114 non-redundant accessions and 5,249 SNP markers. A total of 17 SNPs associated with grain size traits distributed over all the seven chromosomes were revealed with 6D, 5D, and 2D harboring most significant marker–trait associations. Some of the chromosomal regions such as 6D_66.4–71.1 cM, 1D_143.5–156.7 cM, and 2D_89.9–92.5 cM had associations with multiple traits. Candidate genes associated with cell division and differentiation were identified for some of the associated SNP markers. Further efforts to validate these loci will help to understand their role in determining grain size and allelic diversity in current germplasm and its effect on grain size upon transfer to bread wheat background.