Association analysis for resistance to Striga hermonthica in diverse tropical maize inbred lines

Striga hermonthica is a widespread, destructive parasitic plant that causes substantial yield loss to maize productivity in sub-Saharan Africa. Under severe Striga infestation, yield losses can range from 60 to 100% resulting in abandonment of farmers’ lands. Diverse methods have been proposed for Striga management; however, host plant resistance is considered the most effective and affordable to small-scale famers. Thus, conducting a genome-wide association study to identify quantitative trait nucleotides controlling S. hermonthica resistance and mining of relevant candidate genes will expedite the improvement of Striga resistance breeding through marker-assisted breeding. For this study, 150 diverse maize inbred lines were evaluated under Striga infested and non-infested conditions for two years and genotyped using the genotyping-by-sequencing platform. Heritability estimates of Striga damage ratings, emerged Striga plants and grain yield, hereafter referred to as Striga resistance-related traits, were high under Striga infested condition. The mixed linear model (MLM) identified thirty SNPs associated with the three Striga resistance-related traits based on the multi-locus approaches (mrMLM, FASTmrMLM, FASTmrEMMA and pLARmEB). These SNPs explained up to 14% of the total phenotypic variation. Under non-infested condition, four SNPs were associated with grain yield, and these SNPs explained up to 17% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes (Leucine-rich repeats, putative disease resistance protein and VQ proteins) with functions related to plant growth, development, and defense mechanisms. The marker-effect prediction was able to identify alleles responsible for predicting high yield and low Striga damage rating in the breeding panel. This study provides valuable insight for marker validation and deployment for Striga resistance breeding in maize.

Genome-Wide Association Study for Detecting Salt-Tolerance Loci and Candidate Genes in Rice

Salinity is one of the major constraints causing soil problems and is considered a limitation to increased rice production in rice-growing countries. This genome-wide association study (GWAS) experiment was conducted to understand the genetic basis of salt tolerance at the seedling stage in Korean rice. After 10 days of salt stress treatment, salt tolerance was evaluated with a standard evaluation system using a visual salt injury score. With 191 Korean landrace accessions and their genotypes, including 266,040 single-nucleotide polymorphisms (SNPs), using a KNU Axiom Oryza 580K Genotyping Array, GWAS was conducted to detect three QTLs with significant SNPs with a −log10(P) threshold of ≥3.66. The QTL of qSIS2, showed −log10(P) = 3.80 and the lead SNP explained 7.87% of total phenotypic variation. The QTL of qSIS4, showed −log10(P) = 4.05 and the lead SNP explained 10.53% of total phenotypic variation. The QTL of qSIS8 showed −log10(P) = 3.78 and the lead SNP explained 7.83% of total phenotypic variation. Among the annotated genes located in these three QTL regions, five genes were selected as candidates (Os04g0481600, Os04g0485300, Os04g0493000, Os04g0493300, and Os08g0390200) for salt tolerance in rice seedlings based on the gene expression database and their previously known functions.

InDel Marker Development and QTL Analysis of Agronomic Traits in Mung Bean [Vigna Radiate (L.) Wilczek]

The stem color of young mung bean is a very useful tool in germplasm identification. Flowering time and plant height (PH) are known to be strongly correlated with crop adaption and yield. However, few studies have focused on elucidating the genetic mechanisms that regulate these five particular traits: young stem color (YSC), days to first flowering (DFF), days to maturity (DM), PH, and nodes on main stem (NMS). In this study, a genetic linkage map for the F2 population was constructed using 129 InDel markers that were developed based on the sequence variations between parents. A total of 14 QTLs related to YSC, DFF, DM, PH, and NMS were detected. These QTLs were distributed on six chromosomes (1, 3, 4, 6, 7, and 10), which individually accounted for 1.32% to 90.07% of the total phenotypic variation. Using a short and high-density linkage map for the F3 population, six of the seven QTLs which clustered at two intervals on chromosomes 3 and 10 were detected again. Further analysis found that four QTLs between InDel markers R3-15 and R3-19 controlled DFF, DM, PH, and NMS, and each QTL accounted for a large percent of the total phenotypic variation. Analysis of two F2:3 lines also found that the phenotype was highly corresponded to its genotype which is between R3-15 and R3-19. Phenotype and genotype analysis for 30 mung bean accessions showed that the major effect QTL qDFF3 was a key regulator for days to DFF. Using a map-based cloning method, the major effect QTL qYSC4 for YSC was mapped in a 347 Kb interval on chromosome 4. Candidate gene analysis showed that sequence variations and expression level differences existed in the predicted candidate gene between the parents. These results provide a theoretical basis for cloning these QTLs and marker-assisted selection.

Discovery and Fine Mapping of qSCR6.01, a Novel Major QTL Conferring Southern Rust Resistance in Maize

Southern corn rust (SCR), an airborne disease caused by Puccinia polysora, can severely reduce the yield of maize (Zea mays L.). Using recombinant inbred lines (RILs) derived from a cross between susceptible inbred line Ye478 and resistant Qi319 in combination with their high-density genetic map, we located five quantitative trait loci (QTLs) against SCR, designated as qSCR3.04, qSCR5.07, qSCR6.01, qSCR9.03, and qSCR10.01, on chromosomes 3, 5, 6, 9, and 10, respectively. Each QTL could explain 2.84 to 24.15% of the total phenotypic variation. qSCR6.01, detected on chromosome 6, with the highest effect value, accounting for 17.99, 23.47, and 24.15% of total phenotypic variation in two environments and best linear unbiased prediction, was a stably major resistance QTL. The common confidence interval for qSCR6.01 was 2.95 Mb based on the B73 RefGen_v3 sequence. The chromosome segment substitution lines (CSSLs) constructed with Qi319 as the donor parent and Ye478 as the recurrent parent were used to further verify qSCR6.01 resistance to SCR. The line CL183 harboring introgressed qSCR6.01 showed obvious resistance to SCR that was distinctly different from that of Ye478 (P = 0.0038). Further mapping of qSCR6.01 revealed that the resistance QTL was linked to insertion-deletion markers Y6q77 and Y6q79, with physical locations of 77.6 and 79.6 Mb, respectively, on chromosome 6. Different from previous major genes or QTLs against SCR on chromosome 10, qSCR6.01 was a newly identified major QTL resistance to SCR on chromosome 6 for the first time. Using RIL and CSSL populations in combination, the SCR-resistance QTL research can be dissected effectively, which provided important gene resource and genetic information for breeding resistant varieties.

Two Loci from Lycopersicon hirsutum LA407 Confer Resistance to Strains of Clavibacter michiganensis subsp. michiganensis

We used molecular markers to identify quantitative trait loci (QTL) that contribute to resistance to bacterial canker of tomato caused by Clavibacter michiganensis subsp. michiganensis. Resistance was first identified as a marker-trait association in an inbred backcross (IBC) population derived from crossing Lycopersicon hirsutum accession (LA407) with L. esculentum. Single-marker QTL analysis suggested that at least two loci originating from L. hirsutum LA407, Rcm 2.0 on chromosome 2 and Rcm 5.1 on chromosome 5, contribute to resistance in replicated trials. Two segregating F2 populations were developed by crossing resistant inbred backcross lines (IBLs) to elite L. esculentum lines and used to confirm QTL associations detected in the IBC population. In these populations, realized heritability estimates were higher for selection based on maximal disease than for selection based on disease progression. Realized heritability in the population carrying Rcm 2.0 was 0.63 and 0.14, respectively, for each selection criteria. Realized heritability estimates were 0.85 for selection based on maximal disease and 0.37 for selection based on disease progression in a population carrying Rcm 5.1. The disease response of F3 families selected for resistance suggested that both Rcm 2.0 and Rcm 5.1 confer resistance to bacterial strains in the repetitive sequence-based polymerase chain reaction DNA fingerprint classes A and C. Markers linked to Rcm 2.0 explained up to 56% of the total phenotypic variation for resistance in one population, and markers linked to Rcm 5.1 explained up to 73% of the total phenotypic variation for resistance in a separate population.

Gene Estimation, Associations of Traits, and Confirmation of QTL for Common Bacterial Blight Resistance in Common Bean

Common bacterial blight, incited by Xanthomonas campestris pv. phaseoli (Xcp), is a serious disease of common bean(Phaseolus vulgaris L.). Gene estimation, associations of traits, and confirmation of QTL for resistance to Xcp were investigated in a recombinant inbred population derived from the backcross BC2F6 PC-50 (susceptible to Xcp) × XAN-159 (resistant to Xcp). One or two genes from XAN-159 controlled leaf resistance to Xcp. One major gene from XAN-159 was involved in controlling pod resistance to Xcp. Low (+0.24) to intermediate (+0.57 and +0.75) Pearson correlations were observed between leaf and pod reactions to Xcp. Purple flower color was associated with leaf and pod resistance to Xcp but not days to flower. One to 2 QTLs explained from 20 to 51% of the total phenotypic variation for leaf reactions to 5 Xcp strains. Two QTLs explained from 20 to 22% of the total phenotypic variation for pod reactions to Xcp strains EK-11 and DR-7. A marker BC437.1050 was associated with leaf and pod resistance to 5 Xcp strains in nearly all experiments, and accounted for 13% to 45% of the phenotypic variation for these traits. A unassigned marker D13.1000 was associated with only pod resistance to Xcp strains EK-11 and DR-7. Gene number (1 or 2) estimations and number of QTL (1 or 2) detected for resistance to Xcp generally agree. The confirmed marker BC437.1050 is expected to be useful in breeding programs for resistance to Xcp.

Ancestral Contributions to Roasted Peanut Attribute1

Estimates of broad-sense heritability for roasted flavor attribute of peanut (Arachis hypogaea L.) range from 9 to 24% on a single-plot basis. Response to selection is determined by the narrow-sense heritability, calculated from estimates of additive genetic variance which are not available for this trait. One way to assess the additive component of genetic variation is to determine how much of the total phenotypic variation can be predicted from genetic contributions of ancestors of the individuals measured. From 1986 to 1991, samples of 128 peanut cultivars and breeding lines were obtained from peanut research programs representing the three major production areas in the U.S. Samples were roasted to a nearly common color, ground into paste, and assessed for roasted flavor and fruity attribute by a trained sensory panel. CIELAB L* color was also measured for use as a covariate in statistical analysis to adjust for small differences in color. The sum of squares associated with the 128 genotypes accounted for 11% of the total phenotypic variation. Ancestry of the lines was traced back to 47 progenitors for which no further pedigree information was available. Eight progenitors made ancestral contributions that were linearly dependent on the other 39. Ancestral effects accounted for 53% of the genotypic variation, i.e., 6% of the phenotypic variation. Despite shortcomings of this 6% figure as an estimate of narrow-sense heritability for roasted flavor, no other estimates are extant. The residual (nonadditive) variation among genotypes after accounting for ancestral (additive) effects was highly significant. Multiple regression model-building techniques were used to identify 13 ancestors exerting significant effects on roasted flavor. Jenkins Jumbo, F231 (a cross of Dixie Giant with Small White Spanish 3x-2), and Improved Spanish 2B were the only ancestors among the 13 that were common to 40 or more of the 128 lines tested. Jenkins Jumbo was the single most important ancestor, exerting a negative effect on flavor (b = −1.25±0.19). Its progeny would be expected to have roast flavor scores reduced by |b|/2 = 0.62 units and grandprogeny by |b|/4 = 0.31 units. All but four of the 13 ancestors deemed important had deleterious effects on flavor.

The Spatial Pattern and Scale of Variation in Eucalyptus globulus ssp Globulus: Variation in Seedling Abnormalities and Early Growth

Variation in seedling abnormalities and 2- and 4-year growth were studied in a trial in north-westem Tasmania established from 594 open-pollinated families from throughout the geographical range of Eucalyptus globulus Labill. ssp, globulus and populations intergrading with other subspecies. Most (77-80%) of the total (phenotypic) variation in growth traits occurred within families. The genetic variation between families within localities (within c. 10 krn; 13-15% of the total variation), between localities within regions (within c. 100-150 km; c: 4%) and between regions (3-8%) was generally highly significant. However, regional and locality components together accounted for only a small proportion of the total phenotypic variation. Little differentiation was detected between separate sampling sites within localities. Estimates of individual narrow-sense heritabilities were markedly higher than previous reports and were 0.38 for conic volume and 0.41 for height at 4 years, assuming a coefficient of relatedness of 0.4 amongst open-pollinated sibs. On average, progenies from the Otway Ranges region were the fastest growing at the test site, followed by those from King Island. Parent trees with high breeding values were concentrated in the Otway Ranges, Strzelecki Ranges and far southeastem Tasmania with the Bass Strait island localities having intermediate frequencies. Forest fragmentation through clearing for agriculture appears to have had a deleterious effect on the quantitative genetic structure of intergrade populations consistent with high levels of inbreeding. Remnant populations tended to have higher levels of severely abnormal seedlings, higher mortality and poorer growth, and higher heritability estimates and variability both within and between families. Advanced generation hybridisation and inbreeding due to long periods of isolation in small, relict populations may also have had similar effects. Populations sampled are, therefore, likely to have markedly different levels of inbreeding which may have inflated differences between localities and may have important consequences for the exploitation of this material for breeding.