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

Genetic dissection of seed protein concentration in pea using multiple diverse mapping populations

International audienceImproving the seed protein concentration (SPC) of pea is an important breeding objective because of its underlying nutritional value and the demand from the international processing industries. To understand the genetic control ofSPC and support the marker-assisted selection (MAS), we explored three recombinant inbred line (RIL) populations and a genome-wide association study panel (GWAS-2) to identify the quantitative trait loci (QTLs) associated with protein content. The RIL populations used, CDC Amarillo x CDC Limerick (PR-25), MP 1918 x P0540-91 (PR-30), and Ballet x Cameor (PR-31), represent moderate SPC x high SPC crosses. The GWAS-2 panel comprised of representative accessions from global pea breeding programs, pea core germplasm, and commercial cultivars released in Canada. One hundred and ten, and 169 RILs of PR-25 and PR-30, and 233 accessions of GWAS panel were genotyped using a Axiom® 90KSNP array. PR-31 was earlier genotyped using the Genopea 13.2K SNP array [1], and the reported linkage map was used in the current study. Individuals of each mapping population were grown in replicated trials at two to three locationsin Saskatchewan between 2019 and 2021. All mapping populations were tested in 5 to 7 station-years. Seed samples harvested from each plot were used for the determination of SPC using near-infrared (NIR) spectroscopy. We identifiedthree QTLs each in PR-25 [2] and PR-30, and five QTLs in PR-31 associated with SPC. The LOD value of the identified QTLs ranged from 3.0 – 11.0. The QTLs from the biparental populations will be compared with those identified in theGWAS and with the published literatures. The highly significant QTLs identified in this study are useful for MAS of pea breeding lines for SP

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication

Relationships between grain yield and accumulation of biomass, nitrogen and phosphorus in common bean cultivars Relações entre o rendimento de grãos e a acumulação de biomassa, nitrogênio e fósforo em cultivares de feijoeiro

Shoot biomass is considered a relevant component for crop yield, but relationships between biological productivity and grain yield in legume crops are usually difficult to establish. Two field experiments were carried out to investigate the relationships between grain yield, biomass production and N and P accumulation at reproductive stages of common bean (Phaseolus vulgaris) cultivars. Nine and 18 cultivars were grown on 16 m² plots in 1998 and 1999, respectively, with four replications. Crop biomass was sampled at four growth stages (flowering R6, pod setting R7, beginning of pod filling R8, and mid-pod filling R8.5), grain yield was measured at maturity, and N and P concentrations were determined in plant tissues. In both years, bean cultivars differed in grain yield, in root mass at R6 and R7 stages, and in shoot mass at R6 and R8.5, whereas at R7 and R8 differences in shoot mass were significant in 1998 only. In both years, grain yield did not correlate with shoot mass at R6 and R7 and with root mass at R6. Grain yield correlated with shoot mass at R8 in 1999 but not in 1998, with shoot mass at R8.5 and with root mass at R7 in both years. Path coefficient analysis indicated that shoot mass at R8.5 had a direct effect on grain yield in both years, that root mass at R7 had a direct effect on grain yield in 1998, and that in 1999 the amounts of N and P in shoots at R8.5 had indirect effects on grain yield via shoot mass at R8.5. A combined analysis of both experiments revealed that biomass accumulation, N and P in shoots at R6 and R7 as well as root mass at R6 were similar in both years. In 1998 however bean accumulated more root mass at R7 and more biomass and N and P in shoots at R8 and R8.5, resulting in a 57 % higher grain yield in 1998. This indicates that grain yield of different common bean cultivars is not intrinsically associated with vegetative vigor at flowering and that mechanisms during pod filling can strongly influence the final crop yield. The establishment of a profuse root system during pod setting, associated with the continuous N and P acquisition during early pod filling, seems to be relevant for higher grain yields of common bean.<br>A biomassa de parte aérea é considerada um componente relevante para o rendimento dos cultivos, mas é usualmente difícil estabelecer relações entre produção biológica e rendimento de grãos em leguminosas. Foram realizados dois experimentos de campo com o objetivo de investigar as relações entre o rendimento de grãos, a produção de biomassa e a acumulação de N e P em estádios reprodutivos de cultivares de feijoeiro (Phaseolus vulgaris). Nove e 18 cultivares foram cultivadas em 1998 e 1999, respectivamente, em parcelas de 16 m² com quatro repetições. A biomassa foi amostrada em quatro estádios (floração R6, emissão de vagens R7, início de enchimento de vagens R8 e meio de enchimento de vagens R8,5), o rendimento de grãos mensurado na maturação, e foram medidas as concentrações de N e P nos tecidos vegetais. Nos dois anos, as cultivares de feijoeiro diferiram no rendimento de grãos, na massa de raízes nos estádios R6 e R7 e na massa de parte aérea em R6 e R8,5, porém em R7 e R8 apenas em 1998 houve diferenças na massa de parte aérea. Nos dois anos, o rendimento de grãos não se correlacionou com a massa de parte aérea em R6 e R7 e com a massa de raízes em R6. O rendimento de grãos correlacionou-se com a massa de parte aérea em R8 em 1999, com a massa de parte aérea em R8,5 e com a massa de raízes em R7 nos dois anos. Análises de trilha indicaram que a massa de parte aérea em R8,5 exerceu efeito direto no rendimento de grãos nos dois anos, que a massa de raízes em R7 teve efeito direto no rendimento em 1998 e que em 1999 a acumulação de N e P na parte aérea em R8,5 teve efeito indireto no rendimento via massa de parte aérea em R8,5. A análise conjunta dos dois experimentos revelou que a acumulação de massa, N e P na parte aérea em R6 e R7, assim como a massa de raízes em R6, foram similares nos dois anos, mas em 1998 o cultivo acumulou mais massa de raízes em R7 e mais massa, N e P na parte aérea em R8 e R8,5, o que resultou em produção de grãos 57 % superior em 1998. Isso indica que o rendimento de grãos de cultivares de feijoeiro não está intrinsecamente associado com o vigor vegetativo na floração e que mecanismos operantes durante o enchimento das vagens podem influenciar acentuadamente a produção de grãos. O estabelecimento de um profuso sistema radicular durante a emissão de vagens, associado com a contínua aquisição de N e P durante o início de enchimento de vagens, pode assumir relevância para obtenção de maiores rendimentos de grãos na cultura do feijão