Genome-Wide Association Study for Seed Quality Traits in Chickpea

Non-Peer ReviewedChickpeas (Cicer arietinum L.) are an important source of nutrition for the world’s population. Global demand for high quality chickpeas is growing [1]. Canadian chickpea production is expected to increase as a result. Breeding efforts for Canadian varieties are increasingly targeting seed quality. Seed protein and oil content are important, quantitatively inherited traits [2]. To improve nutrition and functional quality of chickpeas an understanding of the genetic basis and underlying traits is crucial. Genome-wide association studies (GWAS) have been employed in breeding populations to aid marker assisted selection (MAS) and genomic selection (GS) applications [3]. A panel of diverse chickpea accessions including materials developed at the Canadian breeding program were grown during the summers of 2016-18. The population was grown at two locations each year, with three replicates per location. The panel was phenotyped for total crude protein and oil content. Over 60K single nucleotide polymorphisms (SNP) derived from whole genome sequences were used to analyze genetic diversity and population structure of the accessions. After data quality screening 170 out of 184 accessions remained, consisting of 45 Desis and 125 Kabulis. Roughly 30 600 SNPs remained after filtering for quality and a 10% minor allele frequency (MAF). Population structure analysis revealed several distinct groups primarily divided by market class. Linkage disequilibrium decay was determined to be between 390 and 380 kilobases. There was a moderate negative correlation shared between the traits (r=-0.57) as well as a genotype by environment interaction. It was determined that year was a greater source of phenotypic variation than growing location. QTLs and candidate genes associated with total protein and oil content were identified through GWAS, with potential markers for both traits on the q arm of chromosome 5

Identification of genes differentially expressed in a resistant reaction to Mycosphaerella pinodes in pea using microarray technology

<p>Abstract</p> <p>Background</p> <p>Ascochyta blight, caused by <it>Mycosphaerella pinodes </it>is one of the most important pea pathogens. However, little is known about the genes and mechanisms of resistance acting against <it>M. pinodes </it>in pea. Resistance identified so far to this pathogen is incomplete, polygenic and scarce in pea, being most common in <it>Pisum </it>relatives. The identification of the genes underlying resistance would increase our knowledge about <it>M. pinodes-</it>pea interaction and would facilitate the introgression of resistance into pea varieties. In the present study differentially expressed genes in the resistant <it>P. sativum </it>ssp. <it>syriacum </it>accession P665 comparing to the susceptible pea cv. Messire after inoculation with <it>M. pinodes </it>have been identified using a <it>M. truncatula </it>microarray.</p> <p>Results</p> <p>Of the 16,470 sequences analysed, 346 were differentially regulated. Differentially regulated genes belonged to almost all functional categories and included genes involved in defense such as genes involved in cell wall reinforcement, phenylpropanoid and phytoalexins metabolism, pathogenesis- related (PR) proteins and detoxification processes. Genes associated with jasmonic acid (JA) and ethylene signal transduction pathways were induced suggesting that the response to <it>M. pinodes </it>in pea is regulated via JA and ET pathways. Expression levels of ten differentially regulated genes were validated in inoculated and control plants using qRT-PCR showing that the P665 accession shows constitutively an increased expression of the defense related genes as peroxidases, disease resistance response protein 39 (DRR230-b), glutathione S-transferase (GST) and 6a-hydroxymaackiain methyltransferase.</p> <p>Conclusions</p> <p>Through this study a global view of genes expressed during resistance to <it>M. pinodes </it>has been obtained, giving relevant information about the mechanisms and pathways conferring resistance to this important disease. In addition, the <it>M. truncatula </it>microarray represents an efficient tool to identify candidate genes controlling resistance to <it>M. pinodes </it>in pea.</p

Variabilidade dos índices de colheita de nutrientes em genótipos de feijoeiro e sua relação com a produção de grãos

A identificação de genótipos com elevada acumulação de biomassa e nutrientes, mas com baixo índice de colheita de nutrientes (razão entre conteúdo de nutrientes nos grãos e na parte aérea), pode reduzir a remoção pelas colheitas e aumentar a sustentabilidade agrícola. Evidências de reduzida variabilidade nos índices de colheita em feijoeiro (Phaseolus vulgaris L.) demandam a avaliação de uma ampla gama de genótipos. Este trabalho teve como objetivo avaliar a variabilidade dos índices de colheita de nutrientes e sua relação com a produção de grãos em genótipos de feijoeiro. Foi conduzido um experimento de campo em Seropédica - RJ, com 64 genótipos de feijoeiro em quatro repetições, incluindo 41 cultivares, 12 linhagens de melhoramento e 10 cultivares locais da região Sul. Os índices de colheita foram mensurados a partir das quantidades acumuladas de biomassa e nutrientes nos grãos, caules e palha de vagens produzidos após trilhagem dos grãos. A média da produção de grãos foi de 205 g m-2, com índices de colheita médios de biomassa, N, P, K, Ca e Mg de 0,62, 0,83, 0,89, 0,58, 0,33 e 0,51 g g-1, respectivamente, denotando intensa translocação de N e P para os grãos, sendo relativamente estreita a variabilidade desses índices. A massa seca de resíduos após trilhagem dos grãos foi em média de 107 g m-2, contendo 2,0, 0,15, 3,6, 2,8 e 1,3 g m-2 de N, P, K, Ca e Mg, respectivamente, o que indica que esses materiais podem restituir quantidades relativamente elevadas de nutrientes em comparação com as demandas do cultivo. Foram obtidas elevadas correlações fenotípicas e genéticas (p < 0,001): positivas entre produção de grãos e índices de colheita de biomassa e N e negativas entre produção e teores de N e P nos grãos. Como as correlações fenotípicas e genéticas entre rendimento e índice de colheita de P foram menos significativas (p < 0,01), foi possível identificar alguns genótipos com baixo índice de colheita de P e bom rendimento. A seleção de genótipos de feijoeiro para maior rendimento de grãos pode resultar em maiores índices de colheita de biomassa e de N, assim como em maiores quantidades de nutrientes nos grãos e menores teores de N e P nos grãos

Genome-Wide Association Study for Seed Quality Traits in Chickpea

Non-Peer ReviewedChickpeas (Cicer arietinum L.) are an important source of nutrition for the world’s population. Global demand for high quality chickpeas is growing [1]. Canadian chickpea production is expected to increase as a result. Breeding efforts for Canadian varieties are increasingly targeting seed quality. Seed protein and oil content are important, quantitatively inherited traits [2]. To improve nutrition and functional quality of chickpeas an understanding of the genetic basis and underlying traits is crucial. Genome-wide association studies (GWAS) have been employed in breeding populations to aid marker assisted selection (MAS) and genomic selection (GS) applications [3]. A panel of diverse chickpea accessions including materials developed at the Canadian breeding program were grown during the summers of 2016-18. The population was grown at two locations each year, with three replicates per location. The panel was phenotyped for total crude protein and oil content. Over 60K single nucleotide polymorphisms (SNP) derived from whole genome sequences were used to analyze genetic diversity and population structure of the accessions. After data quality screening 170 out of 184 accessions remained, consisting of 45 Desis and 125 Kabulis. Roughly 30 600 SNPs remained after filtering for quality and a 10% minor allele frequency (MAF). Population structure analysis revealed several distinct groups primarily divided by market class. Linkage disequilibrium decay was determined to be between 390 and 380 kilobases. There was a moderate negative correlation shared between the traits (r=-0.57) as well as a genotype by environment interaction. It was determined that year was a greater source of phenotypic variation than growing location. QTLs and candidate genes associated with total protein and oil content were identified through GWAS, with potential markers for both traits on the q arm of chromosome 5

Mapping genetic factors affecting the reaction to<i>Xanthomonas axonopodis</i>pv<i>. phaseoli</i>in<i>Phaseolus vulgaris</i>L. under field conditions

The objectives of the present study were to evaluate the field effects of Xanthomonas axonopodis pv. phaseoli (Xap), which causes common bacterial blight (CBB) on common bean (Phaseolus vulgaris L.), and to identify genetic factors for resistance to CBB using a linkage map constructed with random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), simple sequence repeat (SSR), and amplified fragment length polymorphism (AFLP) markers. One hundred and forty-two F2:4lines, derived from a cross between 'OAC Seaforth' and 'OAC 95-4', and the parents were evaluated for their field reaction to CBB. In the inoculated plots, the reaction to CBB was negatively correlated with seed yield, days to maturity, plant height, hypocotyl diameter, pods per plant, and harvest index. A reduction in seed yield and its components was observed when disease-free and CBB-inoculated plots were compared. The broad-sense heritability estimate of the reaction to CBB was 0.74. The disease segregation ratio was not significantly different from the expected segregation ratio for a single locus in an F2generation. The major gene for CBB resistance was localized on linkage group (LG) G5. A simple interval mapping procedure identified three genomic regions associated with the reaction to CBB. One quantitative trait loci (QTL), each on LG G2 (BNG71DraI), G3 (BNG21EcoRV), and G5 (PHVPVPK-1) explained 36.3%, 10.2%, and 42.2% of the phenotypic variation for the reaction to CBB, respectively. Together, these loci explained 68.4% of the phenotypic variation. The relative positions of these QTL on the core common bean map and their comparison with the previous QTL for CBB resistance are discussed.Key words: common bean, molecular markers, common bacterial blight.</jats:p

Genetic diversity among varieties and wild species accessions of pea (<i>Pisum sativum</i>L.) based on molecular markers, and morphological and physiological characters

Random amplified polymorphic DNA, simple sequence repeat, and inter-simple sequence repeat markers were used to estimate the genetic relations among 65 pea varieties (Pisum sativum L.) and 21 accessions from wild Pisum subspecies (subsp.) abyssinicum, asiaticum, elatius, transcaucasicum, and var. arvense. Fifty-one of these varieties are currently available for growers in western Canada. Nei and Li's genetic similarity (GS) estimates calculated using the marker data showed that pair-wise comparison values among the 65 varieties ranged from 0.34 to 1.00. GS analysis on varieties grouped according to their originating breeding programs demonstrated that different levels of diversity were maintained at different breeding programs. Unweighted pair-group method arithmetic average cluster analysis and principal coordinate analysis on the marker-based GS grouped the cultivated varieties separately from the wild accessions. The majority of the food and feed varieties were grouped separately from the silage and specialty varieties, regardless of the originating breeding programs. The analysis also revealed some genetically distinct varieties such as Croma, CDC Handel, 1096M-8, and CDC Acer. The relations among the cultivated varieties, as revealed by molecular-marker-based GS, were not significantly correlated with those based on the agronomic characters, suggesting that the 2 systems give different estimates of genetic relations among the varieties. However, on a smaller scale, a consistent subcluster of genotypes was identified on the basis of agronomic characters and their marker-based GS. Furthermore, a number of variety-specific markers were identified in the current study, which could be useful for variety identification. Breeding strategies to maintain or enhance the genetic diversity of future varieties are proposed.Key words: Pisum sativum, molecular markers, genetic relationships, cluster analysis.</jats:p