Genetics and Genomics of Bacterial Blight Resistance in Rice

Rice is an important food crop for half the world’s population and has been in cultivation for over 10,000 years. During the last few decades, rice has evolved intricate relationships with associated pathogens and pests, bacterial blight (BB) being one of the most important among them. Utilization of resistant varieties with agricultural management practices is a more effective way to control BB. Of the 42 different resistance (R) genes identified to confer BB resistance, 9 have been isolated and cloned, whereas a few of the avirulence genes and a large number of candidate pathogenicity genes have been isolated from Xanthomonas oryzae pv. oryzae. The complete genome sequences of two different rice subspecies japonica and indica and three different races of BB pathogen are available. Therefore, the interaction between rice-Xoo could be deciphered and pave a way to study the molecular aspects of bacterial pathogenesis and host counter measures like innate immunity and R gene–mediated immunity. Although several of the type III effectors of Xoo have been characterized and the host targets of a few of them identified, a relatively large number of candidate effectors remain to be studied and their functional analysis may provide key for developing broad spectrum and durable resistance to BB

Genome wide association studies and candidate gene mining for understanding the genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions

Rice is a high-silica (SiO2·nH2O) accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crops. However, the presence of high silica content is detrimental to rice straw management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in north-western India, and it is eventually burned in situ by farmers, contributing to air pollution. A practical solution could lie in reducing the silica content in rice while also attaining sound plant growth. A set of 258 Oryza nivara accessions along with 25 cultivated varieties of Oryza sativa was used to assess the variation in straw silica content using the molybdenum blue colorimetry method. A large continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08% to 16%, while it varied from 6.18% to 15.81% in the cultivated varieties. The O. nivara accessions containing 43%–54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphisms (SNPs) among 258 O. nivara accessions was used for estimating population structure and genome-wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker-trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported quantitative trait loci (QTL). Twelve out of 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses revealed the presence of promising candidate genes, including those encoding the ATP-binding cassette (ABC) transporter, Casparian thickening, multi-drug and toxin extrusion (MATE) protein, F-box, and MYB-transcription factors. Besides, ortho-QTLs among rice and maize genomes were identified, which could open ways for further genetic analysis of this trait. The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programs to develop rice varieties with lower silica content and higher yield potential

The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question

The wild relatives of rice contain a virtually untapped reservoir of traits that can be used help drive the 21st century green revolution aimed at solving world food security issues by 2050. To better understand and exploit the 23 species of the Oryza genus the rice research community is developing foundational resources composed of: 1) reference genomes and transcriptomes for all 23 species; 2) advanced mapping populations for functional and breeding studies; and 3) in situ conservation sites for ecological, evolutionary and population genomics. To this end, 16 genome sequencing projects are currently underway, and all completed assemblies have been annotated; and several advanced mapping populations have been developed, and more will be generated, mapped, and phenotyped, to uncover useful alleles. As wild Oryza populations are threatened by human activity and climate change, we also discuss the urgent need for sustainable in situ conservation of the genus

High-resolution genetic mapping of QTL governing resistance to corn leaf aphid, Rhopalosiphum maidis (Fitch) in barley

A mapping population, recombinant inbred lines (RILs), was developed from the cross of aphid susceptible cv. PL426 and resistant genotype BK 9816 to identify genetic loci conferring corn leaf aphid (CLA) Rhopalosiphum maidis (Fitch) resistance in barley. RILs showed wide range of aphid infestation (2.2–65.0 aphids/tiller) indicating quantitative inheritance of aphid resistance. All the traits related to aphid resistance, viz. aphid fecundity, chlorophyll content and tiller dry weight of plants, also showed quantitative variation. RILs were further genotyped by sequencing to identify SNPs covering whole barley genome. A total of 605 high-quality bin-mapped SNPs were positioned in seven linkage groups with a total map length of 1208.9 cM and average marker distance of 2.02 cM. Composite interval mapping identified five different quantitative trait loci (QTLs) on chromosomes 1H, 3H, 5H and 6H associated with aphid resistance and related traits. Two QTLs on chromosome 6H, QCLA.pau-6H.1 and QCLA.pau-6H.2, were mapped at genetic intervals of 1.7 cM and 4.9 cM, respectively. QCLA.pau-6H.1 explained 9.76 percent of phenotypic variation for aphid count and 12.78 percent for aphid score. Similarly, QCLA.pau-6H.2 explained 10.96 percent of phenotypic variation for aphid score. The QTL for chlorophyll content and tiller dry weight spanned the same region of QCLA.pau-6H.2, explained 13.08 and 13.20 percent phenotypic variation, respectively. Another QTL associated with chlorophyll content was mapped on chromosome 3H at 3.6-cM interval explained 12.90 percent phenotypic variation. In addition, QTL regions were also identified for aphid resistance and related traits on chromosome 1H and 5H

Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length

Grain weight and grain length are the most stable components of rice yield and important indicators of consumer preference. Considering the potentials of wild rice and to enhance the rice yields to meet the increasing demands, 185 Backcross Inbred Lines (BILs) in the background of O. sativa ssp. indica cv. PR114, including 63 rufi-BILs derived from O. rufipogon IRGC104433 and 122 glumae-BILs from O. glumaepatula IRGC104387 were evaluated for mapping QTLs for yield and yield component traits using Genotyping by Sequencing (GBS). Phenotypic evaluation of BILs in three seasons spanning two locations revealed significant differences compared with recurrent parent. BILs which did not show significant differences for any trait under investigation, or similar based on pedigree, were excluded from GBS. Some glumae-BILs had to be excluded from mapping QTLs due to less sequence information. A custom designed approach for GBS data analysis identified 3322 informative SNPs in 55 rufi-BILs and 3437 informative SNPs in 79 glumae-BILs. QTL mapping identified one QTL for thousand grain weight (qtgw5.1), two for grain width (qgw5.1, qgw5.2) and one for grain length (qgl7.1) in rufi-BILs. In the glumae-BILs, three QTL for thousand grain weight (qtgw2.1, qtgw3.1, qtgw6.1) and two for grain length (qgl3.1, qgl7.1) were identified. Most of the grain weight and width QTL showed positive additive effect contributed by wild species allele, whereas the grain length QTL showed positive additive effect contributed by recurrent parent allele. Based on their physical position, none of the QTLs were found similar to previously cloned QTLs. QTLs for grain traits identified from low yielding wild relatives of rice reveals their significance in improving further the rice yields and widen the genetic base of cultivated rice

Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions

Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop management practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding programs. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions implying substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder’s pool would broaden the genetic base of cultivated rice, thus making the crop more resilient.Land and Food Systems, Faculty ofNon UBCReviewedFacultyResearche

Yield-Enhancing Heterotic QTL Transferred from Wild Species to Cultivated Rice <i>Oryza sativa</i> L

<div><p>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 <i>O. rufipogon</i> and two hybrids (ILH921 and ILH951) having introgressions from <i>O. nivara</i> 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 <i>O. nivara</i> to 7.66 from <i>O. rufipogon</i>. The introgressed regions and their putative association with yield components in hybrids is reported and discussed.</p></div

Mean values of the ILHs for important agronomic traits and extent of heterosis (%) over parents check hybrids and recurrent parents in 17 hybrids.

<p>*, **significant at <i>P≤0.05</i> and <i>P≤0.01</i>, respectively.</p><p>CH1 = PMS17A/Pusa44; CH2 = PMS17A/PR114;</p><p>∧ILH developed from Pusa44 derived IL.</p>∼<p>ILH developed from PR114 derived IL;</p>a<p>details of the hybrids are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096939#pone-0096939-t001" target="_blank">table 1</a>.</p

Performance of 17 introgression lines for important yield contributing traits.

<p>^a Significantly higher and ^c lower than the recurrent parent Pusa 44 or PR114 at <i>P</i>≤0.01.</p><p>^b Significantly higher and ^d lower than the recurrent parent Pusa 44 or PR114 at <i>P</i>≤0.05.</p