Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments

Quantitative trait loci (QTL) analysis could help to identify suitable molecular markers for marker-assisted breeding (MAB). A mapping population of 124 F5:7recombinant inbred lines derived from the cross ‘TAM 112’/‘TAM 111’ was grown under 28 diverse environments and evaluated for grain yield, test weight, heading date, and plant height. The objective of this study was to detect QTL conferring grain yield and agronomic traits from multiple mega-environments. Through a linkage map with 5,948 single nucleotide polymorphisms (SNPs), 51 QTL were consistently identified in two or more environments or analyses. Ten QTL linked to two or more traits were also identified on chromosomes 1A, 1D, 4B, 4D, 6A, 7B, and 7D. Those QTL explained up to 13.3% of additive phenotypic variations with the additive logarithm of odds (LOD(A)) scores up to 11.2. The additive effect increased yield up to 8.16 and 6.57 g m−2 and increased test weight by 2.14 and 3.47 kg m−3 with favorable alleles from TAM 111 and TAM 112, respectively. Seven major QTL for yield and six for TW with one in common were of our interest on MAB as they explained 5% or more phenotypic variations through additive effects. This study confirmed previously identified loci and identified new QTL and the favorable alleles for improving grain yield and agronomic traits.

The Copy Number of Disease-Associated HLA Alleles Predicts the Response to Immunosuppressive Therapy in Acquired Aplastic Anemia

In immune-mediated acquired aplastic anemia (AA), the presence of an HLA allele, which is highly overrepresented or lost due to somatic mutations, may represent a specific immune pathophysiology and a clinical manifestation. HLA-B*14:02 is one of the most overrepresented class I alleles in AA and is also frequently affected by a somatic loss of expression; the inherited B*14:02 genotype was correlated with high-risk clonal evolution in two independent cohorts in the U.S. (Babushok DV et al. Blood Adv 2017; Zaimoku Y et al. manuscript in preparation). In contrast, HLA-B*14:02 is virtually absent in Japanese, in whom somatic mutations of AA have frequently been detected in HLA-B*40:02, B*54:01, and A*02:06, and occasionally in A*02:01, A*02:07, A*31:01, B*13:01, B*40:01, B*40:03, B*44:03, B*55:02, and B*56:01 (Mizumaki H et al. Haematologica 2021). A class II allele HLA-DRB1*15 is highly overrepresented in AA across various ethnic groups, including those in the U.S. and Japanese. This retrospective study in the Japanese population aimed to explore the clinical significance of disease-associated non-B*14:02 HLA class I and II alleles in AA. A total of 423 enrolled patients with AA (very severe [n = 81], severe [n = 266], transfusion dependent non-severe [n = 76]; median age 60 [range, 1-86] years) had undergone genotyping for HLA-A, HLA-B, HLA-C, and HLA-DRB1 at 2-field resolution. The HLA allele frequencies in these patients were compared to those in a Japanese HLA haplotype dataset (n = 19183; Ikeda N et al. Tissue Antigens 2016). The most overrepresented allele in AA was HLA-DRB1*15:02, followed by DRB1*15:01, B*40:02, and A*02:06 (Table); DRB1*13:02 and B*44:03, which are in linkage disequilibrium, were markedly underrepresented, consistent with a well-known protective role of DRB1*13 against autoimmune diseases. HLA-DRB1*15:02 was also significantly correlated with age and its frequency among patients aged <50 years was below the level of the control group (Figure A). Frequencies of HLA-DRB1*15:01, B*40:02, and A*02:06 were increased in both older and younger groups. HLA-A*31:01 and A*02:01 found to be enriched in young patients instead of DRB1*15:02 (Figure B); B*13:01, B*55:02, and B*56:01 showed a similar tendency for an early onset. HLA-B*40:02 was correlated with disease severity and was especially overrepresented in very severe AA (Figure C). The overall response rate to anti-thymocyte globulin-based immunosuppressive therapy at 6 months was 63% (139 of 220 treated and evaluable patients). A trend for a higher response was observed in patients harboring mutation-related HLA-B alleles (except for minor alleles B*13:01, B*40:03, and B*55:02) and the highly overrepresented or protective HLA-DRB1 alleles, but not in the HLA-A alleles (Figure D). A multivariate logistic regression revealed that the combination of the presence of any favorable alleles in HLA-B (odds ratio 3.6, P < 0.0001) or in HLA-DRB1 (odds ratio 2.3, P = 0.00085) was significantly and independently associated with a hematologic response; the tendencies for a lower or higher response in very severe disease and the presence of paroxysmal nocturnal hemoglobinuria clone did not reach statistical significance. Further, there was likely an additive effect when two favorable alleles coexisted in HLA-B or HLA-DRB1 (Figure E); the copy number of the favorable HLA-B and HLA-DRB1 alleles stratified the response rate to four groups: three or four copies, 95% (19 of 20); two copies, 72% (61 of 85); one copy, 59% (50 of 85); and zero copy, 30% (9 of 30). Only eight patients displayed clonal evolution to monosomy 7, myelodysplastic syndrome, or acute myeloid leukemia after immunosuppression without significant overrepresentation or underrepresentation of the pathogenic HLA alleles. Using a large dataset of homogeneous Japanese population with high-resolution HLA typing, we revealed, for the first time, a strong relationship between disease-associated (overrepresented, inactivated, or protecting) HLA alleles and the responsiveness to immunosuppressive therapy. Figure 1 Figure 1. Disclosures Takamatsu: Bristol-Myers Squibb: Honoraria, Research Funding; SRL: Consultancy; Adaptive Biotechnologies, Eisai: Honoraria; Janssen: Consultancy, Honoraria, Research Funding. Yamazaki: Novartis Pharma: Honoraria; Kyowa Kirin: Honoraria; Kyowa Kirin: Research Funding. Nakao: Symbio: Consultancy; Kyowa Kirin: Honoraria; Novartis Pharma: Honoraria; Alexion Pharma: Research Funding.

Identification of Soybean Yield QTL in Irrigated and Rain-Fed Environments

Drought is the primary abiotic stress that limits yield of soybean (Glycine max (L.) Merr.). The study aimed to identify yield-related quantitative trait loci (QTLs) in soybeans using a population of 160 F4-derived lines from ‘Hutcheson’ × PI 471938 crosses, which were cultivated under rain-fed and irrigated conditions. Seed yield was determined based on a total of nine irrigated and five rain-fed environments over two years. Twenty and twenty-seven SSR markers associated with yield (P ≤ 0.05) were identified in the irrigated and rain-fed environments, respectively. Four markers accounted for 22% of the yield variation in the irrigated environments (IR-YLD) and five markers explained 34% of the yield variation in the rain-fed environments (RF-YLD). Two independent IR-YLD and RF-YLD QTLs on chromosome (Chr) 13 (LG-F) were mapped to the Satt395-Sat_074 interval (4.2 cM) and near Sat_375 (3.0 cM), which explained 8% (LOD = 2.6) and 17% (LOD = 5.5) of the yield variation, respectively. The lines homozygous for the Hutcheson allele at the IR-YLD QTL linked to Sat_074 averaged 100 kg ha−1 higher yield than the lines homozygous for the PI 471938 allele. At two independent RF-YLD QTLs on Chr 13 and Chr 17, the lines homozygous for the PI 471938 alleles were 74 to 101 kg ha−1 higher in yield than the lines homozygous for the Hutcheson alleles. Three of the five significant SSR markers associated with RF-YLD were located in a genomic region known for canopy-wilting QTLs, in which the favorable alleles were inherited from PI 471938. The identification of yield-QTLs under the respective rain-fed and irrigated environments provides knowledge regarding differential responses of yield under different irrigation conditions, which will be helpful in developing high-yielding soybean cultivars.

High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping QTLs of Resistance to Aspergillus flavus Infection in Peanut

The cultivated peanut (Arachis hypogaea L.), which is rich in edible oil and protein, is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanuts, hindering the development of the peanut industry and threatening the health of consumers. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for the control of aflatoxin contamination, and understanding the genetic basis of resistance is vital to its genetic enhancement. In this study, we reported the quantitative trait locus (QTL) mapping of resistance to A. flavus infection of a well-known resistant variety, J11. A mapping population consisting of 200 recombinant inbred lines (RILs) was constructed by crossing a susceptible variety, Zhonghua 16, with J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of an infection index in 4 consecutive years, six novel resistant QTLs with 5.03–10.87% phenotypic variances explained (PVE) were identified on chromosomes A05, A08, B01, B03, and B10. The favorable alleles of five QTLs were from J11, while that of one QTL was from Zhonghua 16. The combination of these favorable alleles significantly improved resistance to A. flavus infection. These results could contribute greatly to the understanding of the genetic basis of A. flavus resistance and could be meaningful in the improvement of further resistance in peanuts.

Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines

The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting the use of marker-assisted selection. Presently, two types of genotyping with PVA trait-linked functional markers have been developed and extensively used in breeding programs. The two systems are low throughput gel-based genotyping and genotyping with Kompetitive Allele-Specific PCR (KASP) single nucleotide polymorphism (SNPs) markers. Although the KASP SNPs genotyping was developed to replace the gel-based genotyping, studies have not been conducted to compare the effectiveness of the KASP SNPs markers with the gel-based markers. This study was conducted to assess the carotenoid content of 64 tropical PVA biofortified maize inbred lines containing temperate germplasm in their genetic backgrounds and screen them with both gel-based and KASP markers of PSY1, LCYE and crtRB1 genes. Many of the 64 inbred lines had PVA concentrations surpassing the 15 µg/g provitamin A breeding target set by the HarvestPlus Challenge Program. Favorable alleles of crtRB1, crtRB1 and the KASP SNPs markers were detected in 25 inbred lines with high PVA concentrations. Inbred lines with the favorable alleles of LCYE had the highest concentrations of non-PVA carotenoids, whereas those with the favorable alleles of crtRB1 had high levels of PVA carotenoids. Data from the sequenced region of LCYE revealed one SNP in the first intron that clearly differentiated the high and low β-carotene maize inbred lines. The results of our study demonstrate that the automated KASP SNPs markers can replace the gel-based genotyping for screening a large number of early generation maize inbred lines for PVA content.

Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.

Adaptation assessment of drought tolerance in maize populations from the Sahara in both shores of the Mediterranean Sea

Drought is the main stress for agriculture, and maize (Zea mays L.) germplasm from the Sahara has been identified as potential source of drought tolerance; however, information about adaptation of semitropical maize germplasm from the Sahara to temperate areas has not been reported. Our objective was assessing the adaptation of maize germplasm from Saharan oases as sources of drought tolerance for improving yield and biomass production under drought conditions in temperate environments. A collection of maize populations from Saharan oases was evaluated under drought and control conditions in Spain and Algeria. Algerian populations were significantly different under drought for most traits, and the significant genotype × environment interactions indicated that drought tolerance is genotype-dependent, but tolerance differences among genotypes change across environments. Based on yield, the Algerian maize populations PI527474, PI527478, PI527472, PI527467, PI527470, and PI527473 would be appropriate sources of drought tolerance for temperate environments. Concerning biomass production, the most interesting populations were PI527467, PI542685, PI527478, and PI527472. These Saharan populations could provide favorable alleles for drought tolerance for temperate breeding programs, and could also be used for studying mechanisms and genetic regulation of drought tolerance.

Genetic Mechanisms Determining Grain Number Distribution Along the Spike and Their Effect on Yield Components in Wheat

The number of wheat grains is one of the major determinant of yield. Many quantitative trait loci (QTLs) and some causal genes such as GNI-A1 and WAPO-A1 that are associated with grain number per spike (GNS) have been identified, but the underlying mechanisms remain largely unknown. We analyzed QTLs for grain number and other related traits using 188 doubled haploid lines derived from the Japanese high-yield variety, Kitahonami, as a parent to elucidate the genetic mechanism determining grain number. The major QTLs for grain number at the apical, central and basal parts of the spike were identified in different chromosomal regions. We considered GNI-A1 and WAPO-A1 as candidate genes controlling grain number at the central and basal parts of the spike, respectively. Kitahonami had the favorable 105Y allele of GNI-A1 and WAPO-A1b allele, and unfavorable alleles of QTLs for grain number at the apical part of spikes. Pyramiding the favorable alleles of these QTLs significantly increased GNS without significantly reducing thousand-grain weight (TGW). In contrast, the accumulation of favorable alleles of QTLs for TGW significantly decreased GNS, whereas days to heading positively correlated with GNS. Late heading increased the spikelet number per spike, resulting in a higher GNS. Pyramiding of the QTLs for TGW and days to heading also altered the GNS. In conclusion, GNS is a complex trait controlled by many QTLs, and it is essential for breeding to design.

Combining yield, earliness and plant height in a single genotype: a proposal for breeding in grain sorghum (Sorghum bicolor L.)

Grain sorghum production has expanded during the off-season when rainfall oscillates and becomes insufficient. Aiming to obtain better adapted cultivars, breeding programs have sought new combinations of hybrids with earliness, high grain yield, and ideal plant height for harvesting. This study aimed to estimate de combining ability of grain sorghum lines, proposing a breeding strategy, to identify hybrids gathering high yield, earliness, and desired plant height. Thirty-six hybrids from crosses of 12 lines were evaluated at two sites in the Brazilian region known as Cerrado biome. The evaluated traits were: days to flowering, plant height, and grain yield. For the diallel analysis, Method 4 of Griffing adapted to partial diallel was adopted. By combining ability analysis, we identified promising lines to be used as parents to obtain more yielding, early, and ideal height hybrids. The findings allowed us to propose a breeding strategy, in which complex crosses should be performed to gather favorable alleles in new restorer and male-sterile lines. The hybrids 7, 9, 19, and 22 are the most suitable for growing in the evaluated sites. Highlights: Combining ability analysis allows the identification of promising parents to be used in grain sorghum breeding program. Favorable alleles for each trait are contained in different parents, which makes gene pyramiding a necessary strategy to simultaneously gathering earliness, plant height suitable for harvesting, and high yield in a single hybrid. To improve the R lines, the cross between M2 (good donor for shorter height) x M5 (good donor for earliness) should be performed, and the hybrid resulting from M2xM5 can be crossed with the M4 line (good donor for high grain yield). The hybrid generated by the cross F1-B x F4-B (high earliness) should be crossed with the hybrid derived from F6-B x F5-B (shorter height), and the hybrid resulting should be crossed with the hybrid generated by F2-B x F3-B (high grain yield).

Genome-Wide Association Study of the Genetic Basis of Effective Tiller Number in Rice

Background Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield. ETN is a complex quantitative trait regulated by both genetic and environmental factors. Despite multiple tillering-related genes have been cloned previously, few of them have been utilized in practical breeding programs. Results In this study, we conducted a genome-wide association study (GWAS) for ETN using a panel of 490 rice accessions derived from the 3 K rice genomes project. Thirty eight ETN-associated QTLs were identified, interestingly, four of which colocalized with the OsAAP1, DWL2, NAL1, and OsWRKY74 gene previously reported to be involved in rice tillering regulation. Haplotype (Hap) analysis revealed that Hap5 of OsAAP1, Hap3 and 6 of DWL2, Hap2 of NAL1, and Hap3 and 4 of OsWRKY74 are favorable alleles for ETN. Pyramiding favorable alleles of all these four genes had more enhancement in ETN than accessions harboring the favorable allele of only one gene. Moreover, we identified 25 novel candidate genes which might also affect ETN, and the positive association between expression levels of the OsPILS6b gene and ETN was validated by RT-qPCR. Furthermore, transcriptome analysis on data released on public database revealed that most ETN-associated genes showed a relatively high expression from 21 days after transplanting (DAT) to 49 DAT and decreased since then. This unique expression pattern of ETN-associated genes may contribute to the transition from vegetative to reproductive growth of tillers. Conclusions Our results revealed that GWAS is a feasible way to mine ETN-associated genes. The candidate genes and favorable alleles identified in this study have the potential application value in rice molecular breeding for high ETN and grain yield.