Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects

The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability

Genetic diversity of crocus sativus and its close relative species analyzed by iPBS-retrotransposons

Saffron (Crocus L.) is a member of Crocoideae, the biggest of four subfamilies in the Iridaceae family. It has 2n = 3x = 24 chromosomes and is triploid; thus, it is sterile. In previous research, different molecular DNA markers were used but molecular characterization and genetic diversity of this complex genus have not yet been clarified. Therefore, current study aimed to determine the molecular characterization of saffron and its close relative species using inter-primer binding site (iPBS)-retrotransposon markers. Eighty-three iPBS-retrotransposon primers were used in 28 C. sativus genotypes and 17 close relative species of saffron to identify their genetic diversity. Sixteen polymorphic iPBS-retrotransposon primers generated a total of 401 polymorphic scorable bands. The mean PIC value, Nei’s genetic diversity and Shannon’s information index (I) were calculated as 0.85, 0.16 and 0.29, respectively. The results of the Unweighted Pair Group Method with Arithmetic mean UPGMA dendrogram and Principal Coordinates Analysis PCoA analysis indicated a spatial representation of the relative genetic distances among 28 saffron samples and the 17 close relative species were categorized under two distinct groups. Saffron genotypes showed very limited genetic variation and according to the iPBS-retrotransposon data, its close relatives were C. cartwrightianus and C. pallasii subsp. pallasii. © 2017, Society of Field Crops Science. All rights reserved.Firat University Scientific Research Projects Management Unit: FBA-2014-2704The authors express their gratitude to University of Cukurova, Scientific Research Projects Unit for their financial support (FBA-2014-2704). -

SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73.

Endogenous Plastic Somatic (ePS) cells isolated from adult human tissues exhibit extensive lineage plasticity in vitro and in vivo. Here we visualize these rare ePS cells in a latent state, i.e. lacking SOX2, OCT3/4 and NANOG (SON) expression, in non-diseased breast specimens through immunohistochemical analysis of previously identified ePS-specific biomarkers (CD73+, EpCAM+ and CD90-). We also report a novel mechanism by which these latent ePS cells acquire SON expression and plasticity in vitro. Four extracellular factors are necessary for the acquisition of SON expression and lineage plasticity in ePS cells: adenosine (which is produced by the 5' ecto-nucleotidase CD73 and activates in turn the PKA-dependent IL6/STAT3 pathway through the adenosine receptor ADORA2b), IL6, FGF2 and ACTIVIN A. Blocking any pathway component renders ePS cells incapable of SON expression and lineage plasticity. Notably, hESCs do not use adenosine or IL6 nor they express CD73 or ADORA2b and inhibition of adenosine signaling does not ablate their plasticity. Therefore, the data presented here delineate novel circuitry and physiological signals for accessing SON expression in rare, undifferentiated human cells

SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73.

Endogenous Plastic Somatic (ePS) cells isolated from adult human tissues exhibit extensive lineage plasticity in vitro and in vivo. Here we visualize these rare ePS cells in a latent state, i.e. lacking SOX2, OCT3/4 and NANOG (SON) expression, in non-diseased breast specimens through immunohistochemical analysis of previously identified ePS-specific biomarkers (CD73+, EpCAM+ and CD90-). We also report a novel mechanism by which these latent ePS cells acquire SON expression and plasticity in vitro. Four extracellular factors are necessary for the acquisition of SON expression and lineage plasticity in ePS cells: adenosine (which is produced by the 5' ecto-nucleotidase CD73 and activates in turn the PKA-dependent IL6/STAT3 pathway through the adenosine receptor ADORA2b), IL6, FGF2 and ACTIVIN A. Blocking any pathway component renders ePS cells incapable of SON expression and lineage plasticity. Notably, hESCs do not use adenosine or IL6 nor they express CD73 or ADORA2b and inhibition of adenosine signaling does not ablate their plasticity. Therefore, the data presented here delineate novel circuitry and physiological signals for accessing SON expression in rare, undifferentiated human cells

Genome-wide association studies of Ca and Mn in the seeds of the common bean (Phaseolus vulgaris L.)

PubMed: 32763354SNP markers linked to genes controlling Ca and Mn uptake were identified in the common bean seeds using DArT-based association mapping (AM). The Ca concentration in the seeds varied between 475 and 3,100 mg kg?1 with an average of 1,280.9 mg kg?1 and the Mn concentration ranged from 4.87 to 27.54 mg kg?1 with a mean of 11.76 mg kg?1. A total of 19,204 SNP markers were distributed across 11 chromosomes that correspond to the haploid genome number of the common bean. The highest value of ?K was determined as K = 2, and 173 common bean genotypes were split into two main subclusters as POP1 (Mesoamerican) and POP2 (Andean). The results of the UPGMA dendrogram and PCA confirmed those of STRUCTURE analysis. MLM based on the Q + K model identified a large number of markers-trait associations. Of the 19,204 SNPs, five (on Pv2, 3, 8, 10 and 11) and four (on Pv2, 3, 8 and 11) SNPs were detected to be significantly related to the Ca content of the beans grown in Bornova and Menemen, respectively in 2015. In 2016, six SNPs (on Pv1–4, 8 and 10) were identified to be significantly associated with the Ca content of the seeds obtained from Bornova and six SNPs (on Pv1–4, 8 and 10) from Menemen. Eight (on Pv3, 5 and 11) and four (on Pv2, 5 and 11) SNPs had a significant association with Mn content in Bornova in 2015 and 2016, respectively. In Menemen, eight (on Pv3, 5, 8 and 11) and 11 (on Pv1, 2, 5, 10 and 11) SNPs had a significant correlation with Mn content in 2015 and 2016, respectively. © 2020 Elsevier Inc.Türkiye Bilimsel ve Teknolojik Araştirma Kurumu, TÜBITAK: TUBITAK-114O555The study was financially supported by The Scientific and Technological Research Council of Turkey (TUBITAK) with project no TUBITAK-114O555 . We would like to especially thank Paul Gepts from the University of California-Davis (USA) for kindly sharing his control group of common bean accessions (the Mesoamerican and Andean gene pools)

QTL mapping of genome regions controlling manganese uptake in Lentil Seed

PubMedID: 29588380This study evaluated Mn concentration in the seeds of 120 RILs of lentil developed from the cross "CDC Redberry" × "ILL7502". Micronutrient analysis using atomic absorption spectrometry indicated mean seed manganese (Mn) concentrations ranging from 8.5 to 26.8 mg/kg, based on replicated field trials grown at three locations in Turkey in 2012 and 2013. A linkage map of lentil was constructed and consisted of seven linkage groups with 5,385 DNA markers. The total map length was 973.1 cM, with an average distance between markers of 0.18 cM. A total of 6 QTL for Mn concentration were identified using composite interval mapping (CIM). All QTL were statistically significant and explained 15.3-24.1% of the phenotypic variation, with LOD scores ranging from 3.00 to 4.42. The high-density genetic map reported in this study will increase fundamental knowledge of the genome structure of lentil, and will be the basis for the development of micronutrient-enriched lentil genotypes to support biofortification efforts. © 2018 Ates et al.The study was supported by The Scientific and Technological Research Council of Turkey (TUBITAK), project no. COST-111O446. The authors declare that they have no conflicts of interest

Identification of markers associated with traits for use in marker-assisted selection in saffron

Odredivanje veze izmedu molekularnih markera i agronomskih osobina predstavlja odlican alat za selekciju pomo u markera. U ovoj studiji, multivarijantna stepenasta regresiona analiza korišcena je za procenu veze izmedu SSR markera i nekih agronomskih osobina u ekotipovima šafrana. a analize asocijacija koriš ene su dvogodišnje prosecne vrednosti za izmerene osobine. Rezultati postupne analize regresije otkrili su znacajnu asocijaciju izmedu osobina i proucavanih lokusa. Identifikovano je ukupno 25 SSR markera. Markeri SCA382, SCA15 i SCD219 bili su povezani sa ve inom osobina, i mogu se koristiti kao kandidat markeri u selekciji pomo u molekularnih markera. © 2018, Serbian Genetics Society.Determination of association between molecular markers and agronomic traits provides an excellent tool for marker-assisted selection. In this study, multivariate stepwise regression analysis was used to estimate associations between SSR markers and some agronomic traits in saffron ecotypes. Two-year average values for the measured traits were used for association analyses. The results of stepwise regression analysis revealed significant associations between the traits and some of the studied loci. More than one informative marker was detected for most of the traits. Totally 25 informative SSR markers were identified in two years. Markers SCA382, SCA15 and SCD219 were associated with most traits under both years. These markers are considered to be relatively more reliable. Among the SSR primers, special attention should be drawn to primers SCA382, SCA15, and SCD219, which had the highest associated fragments with most traits in two years and could be considered for use as candidate markers in marker-assisted selection. © 2018, Serbian Genetics Society

Evidence That an HMGA1 Gene Variant Associates with Type 2 Diabetes, Body Mass Index, and High-Density Lipoprotein Cholesterol in a Hispanic-American Population

WOS: 000330808200004PubMed ID: 24148075Background: High-mobility group AT-hook 1 (HMGA1) is an important regulator of the insulin receptor gene. We have previously shown in three populations of white European ancestry that the HMGA1 gene variant rs146052672 (also designated IVS5-13insC) is associated with type 2 diabetes mellitus (T2DM). The aim of this study was to measure the frequency of this variant and to determine the degree of the association with T2DM and other features of the metabolic syndrome in a replication cohort of Hispanic Americans. Methods: This was a retrospective cohort study of well-characterized Hispanic-American participants analyzed in the Genomic Resource in Atherosclerosis (GRA) (Cardiovascular Research Institute, University of California, San Francisco). A total of 1144 individuals were studied, 320 of whom had T2DM. We examined associations of the rs146052672 SNP with T2DM, plasma lipids, lipoproteins, and body mass index (BMI). Results: In this Hispanic-American cohort, the HMGA1 rs146052672 minor allele (C-insertion) frequency (MAF) was 21.4% with a carrier frequency of 37.4%, considerably higher than we previously observed among GRA white Europeans (MAF 3.1%). The prevalence of the IVS5-13insC variant was significantly higher in those with T2DM compared to controls [42.2% vs. 35.5%; odds ratio (OR) 1.44 95% confidence interval (CI) 1.09-1.90, P=0.011). The variant was also associated with BMI (positively, P=0.045) and plasma high-density lipoprotein cholesterol (HDL-C) (negatively, P=0.047). Conclusions: As we saw previously among white Europeans, a functional HMGA1 variant was associated with T2DM in individuals of Hispanic-American ethnicity and was present at a much higher frequency.Diabetes Research Fund of Mount Zion Health Fund; Jewish Community Endowment Fund; Hellman Family Award; UCSF; Campini Foundation; Joseph Drown FoundationThis work was supported by the Diabetes Research Fund of Mount Zion Health Fund, a supporting foundation of the Jewish Community Endowment Fund (I.D.G. and C.R.P.), a Hellman Family Award (C.R.P.), a UCSF Academic Senate Award (C.R.P.), the Campini Foundation, the Joseph Drown Foundation (M.J.M.), and by gifts from Peter Read, Donald Yellon, and the Mildred V. Strouss Charitable Trust