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Wheat blast caused by Pyricularia oryzae pathotype Triticum (MoT) has been transmitted from South America to Bangladesh and Zambia and is now spreading in these countries. To prepare against its further spread to Asian countries, we introduced Rmg8, a gene for resistance to wheat blast, into a Japanese elite cultivar, Chikugoizumi (ChI), through recurrent backcrosses and established ChI near-isogenic lines, #2-1-10 with the Rmg8/Rmg8 genotype and #4-2-10 with the rmg8/rmg8 genotype. A molecular analysis suggested that at least 96.6% of the #2-1-10 genome was derived from the recurrent parent ChI. The #2-1-10 line was resistant to MoT not only in primary leaves at the seedling stage but also in spikes and flag leaves at the heading stage. The strength of the resistance in spikes of this Rmg8 carrier was comparable to that of a carrier of the 2NS segment, which has been the only genetic resource released to farmers' fields for wheat blast resistance. On the other hand, the 2NS resistance was not expressed on leaves at the seedling stage nor flag leaves at the heading stage. Considering that leaf blast has been increasingly reported and regarded as an important inoculum source for spike blast, Rmg8 expressed at both the seedling and heading stages, or more strictly in both leaves and spikes, is suggested to be useful to prevent the spread of MoT in Asia and Africa. [ABSTRACT FROM AUTHOR]

At the major vernalization locus ‘Vrn-D1’, the spring allele, Vrn-D1a, and two winter alleles, Vrn-D1b and vrn-D1, have been identified in wheat. We conducted field trials to determine the effects of alleles on growth and yield-related traits, using near-isogenic lines developed in the genetic background of spring type wheat cultivars, ‘Abukumawase’ and ‘Asakazekomugi’, both of which carry the Vrn-D1a allele. Although maturity date of three alleles was same, the panicle development occurred earlier in the following order of genotype: Vrn-D1a > Vrn-D1b > vrn-D1. There was a significant difference in panicle development even between two winter type alleles vrn-D1 and Vrn-D1b. Grain yield and the spikelet number per spike of the original spring type cultivars were lower than those of the winter type NILs. In addition, while the young panicle development of the tillers in the spring type cultivars was found to be two weeks to one month later in the tillers than that in the main stem, young panicle development of the main stem and tillers in the winter type NILs were almost identical. Hence, winter type wheat bearing vrn-D1 which exhibit later panicle development than that bearing Vrn-D1b, was elucidated to might be more useful especially in areas with high risk of frost damage. Spring type wheat had a lower sink capacity and grain yield, meanwhile that was considered to prevent severe frost damage by allowing late-developed tillers to survive.

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of "Mibaek 2ho" variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the "Mibaek 2ho" variety waxy maize. [ABSTRACT FROM AUTHOR]

At the major vernalization locus 'Vrn-D1', the spring allele, Vrn-D1a, and two winter alleles, Vrn-D1b and vrn-D1, have been identified in wheat. We conducted field trials to determine the effects of alleles on growth and yield-related traits, using near-isogenic lines developed in the genetic background of spring type wheat cultivars, 'Abukumawase' and 'Asakazekomugi', both of which carry the Vrn-D1a allele. Although maturity date of three alleles was same, the panicle development occurred earlier in the following order of genotype: Vrn-D1a > Vrn-D1b > vrn-D1. There was a significant difference in panicle development even between two winter type alleles vrn-D1 and Vrn-D1b. Grain yield and the spikelet number per spike of the original spring type cultivars were lower than those of the winter type NILs. In addition, while the young panicle development of the tillers in the spring type cultivars was found to be two weeks to one month later in the tillers than that in the main stem, young panicle development of the main stem and tillers in the winter type NILs were almost identical. Hence, winter type wheat bearing vrn-D1 which exhibit later panicle development than that bearing Vrn-D1b, was elucidated to might be more useful especially in areas with high risk of frost damage. Spring type wheat had a lower sink capacity and grain yield, meanwhile that was considered to prevent severe frost damage by allowing late-developed tillers to survive. [ABSTRACT FROM AUTHOR]

The brown planthopper (Nilaparvata lugens Stål, BPH) is the most destructive pest of rice (Oryza sativa L.). Utilizing resistant rice cultivars that harbor resistance gene/s is an effective strategy for integrated pest management. Due to the co-evolution of BPH and rice, a single resistance gene may fail because of changes in the virulent BPH population. Thus, it is urgent to explore and map novel BPH resistance genes in rice germplasm. Previously, an indica landrace from India, Paedai kalibungga (PK), demonstrated high resistance to BPH in both in Wuhan and Fuzhou, China. To map BPH resistance genes from PK, a BC1F2:3 population derived from crosses of PK and a susceptible parent, Zhenshan 97 (ZS97), was developed and evaluated for BPH resistance. A novel BPH resistance locus, BPH39, was mapped on the short arm of rice chromosome 6 using next-generation sequencing-based bulked segregant analysis (BSA-seq). BPH39 was validated using flanking markers within the locus. Furthermore, near-isogenic lines carrying BPH39 (NIL-BPH39) were developed in the ZS97 background. NIL-BPH39 exhibited the physiological mechanisms of antibiosis and preference toward BPH. BPH39 was finally delimited to an interval of 84 Kb ranging from 1.07 to 1.15 Mb. Six candidate genes were identified in this region. Two of them (LOC_Os06g02930 and LOC_Os06g03030) encode proteins with a similar short consensus repeat (SCR) domain, which displayed many variations leading to amino acid substitutions and showed higher expression levels in NIL-BPH39. Thus, these two genes are considered reliable candidate genes for BPH39. Additionally, transcriptome sequencing, DEGs analysis, and gene RT-qPCR verification preliminary revealed that BPH39 may be involved in the jasmonic acid (JA) signaling pathway, thus mediating the molecular mechanism of BPH resistance. This work will facilitate map-based cloning and marker-assisted selection for the locus in breeding programs targeting BPH resistance. [ABSTRACT FROM AUTHOR]

Chlorfenapyr is a broad‐spectrum halogenated pyrrole insecticide with a unique mode of action. Due to the misuse and overuse of this chemical, resistance has been reported in several arthropods, including Plutella xylostella, which is one of the most destructive insect pests afflicting crucifers worldwide. A better understanding of the cross‐resistance and genetics of field‐evolved chlorfenapyr resistance could effectively guide resistance management practices. Here, the chlorfenapyr resistance of a field‐derived population of P. xylostella was introgressed into the susceptible IPP‐S strain using a selection‐assisted multigenerational backcrossing approach. The constructed near‐isogenic strain, TH‐BC5F2, shared 98.4% genetic background with the recurrent parent IPP‐S strain. The TH‐BC5F2 strain showed 275‐fold resistance to chlorfenapyr, but no significant cross‐resistance to spinosad, abamectin, chlorpyrifos, β‐cypermethrin, indoxacarb, chlorantraniliprole, or broflanilide (no more than 4.2‐fold). Genetic analysis revealed that resistance was autosomal, incompletely dominant, and conferred by 1 major gene or a few tightly linked loci. The synergism of metabolic inhibitors (PBO, DEM, and DEF) to chlorfenapyr was very weak (<1.7‐fold), and the metabolic enzyme activities in the TH‐BC5F2 strain were not significantly elevated compared with the IPP‐S strain. The results enhances our understanding of the genetic traits of chlorfenapyr resistance, and provides essential information for improving resistance management strategies. [ABSTRACT FROM AUTHOR]

The fruit flesh of watermelons differs depending on the distinct carotenoid composition. Orange-colored flesh relates to the accumulation of β-carotene, which is beneficial to human health. Canary-yellow-fleshed OTO-DAH and orange-β-fleshed (orange-fleshed with high β-carotene) NB-DAH near-isogenic lines (NILs) were used to determine the genetic mechanism attributed to orange watermelon flesh. For genetic mapping, an F2 population was developed by crossing the two NILs. The segregation ratio of flesh color in the F2 population indicated that the orange-β flesh of the NB-DAH NIL was controlled by a single incompletely dominant gene. Through a comparative analysis of the whole-genome sequences of the parent lines and NILs, a major introgression region unique to the NB-DAH NIL was detected on Chr. 1; this was considered a candidate region for harboring genes that distinguish orange from canary-yellow and red flesh. Among the 13 genes involved in the carotenoid metabolic pathway in watermelons, only ClPSY1 (ClCG01G008470), which encodes phytoene synthase 1, was located within the introgression region. The genotyping of F2 plants using a cleaved amplified polymorphic sequence marker developed from a non-synonymous SNP in ClPSY1 revealed its relationship with orange-β flesh. The insights gained in this study can be applied to marker-assisted breeding for this desirable trait. [ABSTRACT FROM AUTHOR]

Significance Statement: Superior natural alleles of Mediator subunit genes have efficacy to develop desirable semi‐dwarf chickpea cultivars by modulating lignin and phenylpropanoid biosynthesis without compromising agronomic performance. [ABSTRACT FROM AUTHOR]

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of “Mibaek 2ho” variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the “Mibaek 2ho” variety waxy maize.

ABSTRACTIn Kenya and many other African countries, improving rice productivity is vital for future food security. To improve rice productivity in Kenya, near-isogenic lines (NIL) were developed by introducing Gn1a and WFP, genes that function to increase grain number per panicle by increasing secondary and primary rachis-branches, into NERICA 1, a registered variety in Kenya. The aim of this study was to determine whether the introduction of these genes has the potential to improve rice productivity under tropical highland conditions in central Kenya. Field experiments were conducted in 2016 and 2017 at a lowland rice field in Mwea, Kenya, under different nitrogen fertilization conditions using three lines of NERICA 1 introgressed with Gn1a and/or WFP (NIL-Gn1a, NIL-WFP, and NIL-Gn1a+WFP) and their recurrent parents, NERICA 1. Two years of field experiments revealed that the introgression lines enhanced grain yield by increasing the number of primary and secondary rachis-branches and the number of grains per panicle. Gn1a and WFP showed additive effects and the introgression of both genes alleviated the negative effects on yield components observed in the introgressed lines, resulting in higher grain yield. Sufficient nitrogen fertilization was required to increase yield in the single-gene introgression lines. However, the line with both Gn1a and WFP achieved reasonable yields even under low fertilizer conditions in Mwea, Kenya. As these introgression lines have similar growing characteristics to their parent variety, they are expected to contribute to increased rice production in Kenya and similar environments in sub-Saharan Africa.

In Kenya and many other African countries, improving rice productivity is vital for future food security. To improve rice productivity in Kenya, near-isogenic lines (NIL) were developed by introducing Gn1a and WFP, genes that function to increase grain number per panicle by increasing secondary and primary rachis-branches, into NERICA 1, a registered variety in Kenya. The aim of this study was to determine whether the introduction of these genes has the potential to improve rice productivity under tropical highland conditions in central Kenya. Field experiments were conducted in 2016 and 2017 at a lowland rice field in Mwea, Kenya, under different nitrogen fertilization conditions using three lines of NERICA 1 introgressed with Gn1a and/or WFP (NIL-Gn1a, NIL-WFP, and NIL-Gn1a+WFP) and their recurrent parents, NERICA 1. Two years of field experiments revealed that the introgression lines enhanced grain yield by increasing the number of primary and secondary rachis-branches and the number of grains per panicle. Gn1a and WFP showed additive effects and the introgression of both genes alleviated the negative effects on yield components observed in the introgressed lines, resulting in higher grain yield. Sufficient nitrogen fertilization was required to increase yield in the single-gene introgression lines. However, the line with both Gn1a and WFP achieved reasonable yields even under low fertilizer conditions in Mwea, Kenya. As these introgression lines have similar growing characteristics to their parent variety, they are expected to contribute to increased rice production in Kenya and similar environments in sub-Saharan Africa. [ABSTRACT FROM AUTHOR]

ABSTRACTThe total spikelet number (TSN) per panicle is an essential factor involved in grain yield among yield components in rice. IR64-NIL12 carrying qTSN12.2-YP4, which was detected on chromosome 12 for TSN per panicle, has been developed in a previous study. It is important to characterize the environment of gene function to increase yields. Thus, we attempted to evaluate IR64-NIL12 grown under no, low, and high fertilizer conditions in 2019 and 2020. Grain yields of IR64-NIL12 were significantly higher than that of IR64 in all conditions. The average grain yield of each condition for IR64 and IR64-NIL12 ranged from 387 to 616 g m−2. Therefore, qTSN12.2-YP4 would have an increasing effect on grain yield within this range. The ratio of fertility improved in IR64-NIL12. This rice line exhibited modified traits, such as tiller number and plant height (during the vegetative stage), as well as panicle number (at maturity), which may confer an advantage in terms of light-intercepting characteristics. We also focused on the number of unproductive tillers and dry weight per tiller at the heading stage to investigate the mechanism of the increasing effect of qTSN12.2-YP4 on TSN per panicle. There is a significant difference in dry weight per tiller at heading between IR64 and IR64-NIL12, but not in the percentage of unproductive tillers. Therefore, this result indicated that qTSN12.2-YP4 contributes to increasing dry weight per tiller until the heading stage and, consequently, TSN per panicle.

Magnaporthe oryzae is known for its genetic diversity and pathogenic variability, leading to rapid breakdown of resistance in rice. Incorporating multiple broad-spectrum blast resistance genes into rice cultivars would extend disease resistance longevity. Effective resistance breeding in rice therefore requires continual enrichment of the reservoir of resistance genes and alleles. We conducted a large-scale screen of rice blast resistance in about 2 000 rice accessions. Among them, 247 accessions showed at least medium resistance to the natural infection of rice blast and 7 novel Pik alleles were identified from them. Variations in gene sequences were then correlated with the phenotypic trait to enable the identification of favorable alleles. Among the seven novel Pik alleles, the resistant rate of Pik-R0/ME/7017 donors was greater than 80%, and the disease score was less than 3. Through molecular marker-assisted backcross breeding, we successfully transferred the three Pik alleles, Pik-R0/ME/7017, into an elite cultivated line Kongyu 131 to obtain BC3F2 lines, which showed enhanced resistance to rice blast compared with the recurrent parent. Assessment of these near-isogenic lines in the greenhouse using 31 isolates of M. oryzae from Heilongjiang Province of China revealed that the resistant levels of the BC3F2 lines with Pik-R0/ME/7017 were significantly higher than those of the established cloned resistance genes Pik-m and Pi1. Exploring such alleles will enrich our gene library for resistance to rice blast.

The total spikelet number (TSN) per panicle is an essential factor involved in grain yield among yield components in rice. IR64-NIL12 carrying qTSN12.2-YP4, which was detected on chromosome 12 for TSN per panicle, has been developed in a previous study. It is important to characterize the environment of gene function to increase yields. Thus, we attempted to evaluate IR64-NIL12 grown under no, low, and high fertilizer conditions in 2019 and 2020. Grain yields of IR64-NIL12 were significantly higher than that of IR64 in all conditions. The average grain yield of each condition for IR64 and IR64-NIL12 ranged from 387 to 616 g m−2. Therefore, qTSN12.2-YP4 would have an increasing effect on grain yield within this range. The ratio of fertility improved in IR64-NIL12. This rice line exhibited modified traits, such as tiller number and plant height (during the vegetative stage), as well as panicle number (at maturity), which may confer an advantage in terms of light-intercepting characteristics. We also focused on the number of unproductive tillers and dry weight per tiller at the heading stage to investigate the mechanism of the increasing effect of qTSN12.2-YP4 on TSN per panicle. There is a significant difference in dry weight per tiller at heading between IR64 and IR64-NIL12, but not in the percentage of unproductive tillers. Therefore, this result indicated that qTSN12.2-YP4 contributes to increasing dry weight per tiller until the heading stage and, consequently, TSN per panicle. [ABSTRACT FROM AUTHOR]

Summary: Global warming is a major abiotic stress factor, which limit rice production. Exploiting the genetic basis of the natural variation in heat resistance at different reproductive stages among diverse exotic Oryza germplasms can help breeding heat‐resistant rice cultivars. Here, we identified a stable quantitative trait locus (QTL) for heat tolerance at the heading stage on chromosome 5 (qHTH5) in O. rufipogon Griff. The corresponding gene, HTH5, pertains to the pyridoxal phosphate‐binding protein PLPBP (formerly called PROSC) family, which is predicted to encode pyridoxal phosphate homeostasis protein (PLPHP) localized to the mitochondrion. Overexpression of HTH5 increased the seed‐setting rate of rice plants under heat stress at the heading stage, whereas suppression of HTH5 resulted in greater susceptibility to heat stress. Further investigation indicated that HTH5 reduces reactive oxygen species accumulation at high temperatures by increasing the heat‐induced pyridoxal 5'‐phosphate (PLP) content. Moreover, we found that two SNPs located in the HTH5 promoter region are involved with its expression level and associated with heat tolerance diversity. These findings suggest that the novel gene HTH5 might have great potential value for heightening rice tolerance to heat stress to the on‐going threat of global warming. [ABSTRACT FROM AUTHOR]

The stigma exsertion rate (SER) is a complex agronomy phenotype controlled by multiple genes and climate and a key trait affecting the efficiency of hybrid rice seed production. Using a japonica two-line male sterile line (DaS) with a high SER as the donor and a tropical japonica rice (D50) with a low SER as the acceptor to construct a near-isogenic line [NIL (qSE4DaS)]. Populations were segregated into 2,143 individuals of BC3F2 and BC4F2, and the stigma exsertion quantitative trait locus (QTL) qSE4 was determined to be located within 410.4 Kb between markers RM17157 and RM17227 on chromosome 4. Bioinformatic analysis revealed 13 candidate genes in this region. Sequencing and haplotype analysis indicated that the promoter region of LOC_Os04g43910 (ARF10) had a one-base substitution between the two parents. Further Reverse Transcription-Polymerase Chain Reaction (RT-PCR) analysis showed that the expression level of ARF10 in DaS was significantly higher than in D50. After knocking out ARF10 in the DaS background, it was found that the SER of arf10 (the total SER of the arf10- 1 and the arf10-2 were 62.54 and 66.68%, respectively) was significantly lower than that of the wild type (the total SER was 80.97%). Transcriptome and hormone assay analysis showed that arf10 had significantly higher auxin synthesis genes and contents than the wild type and the expression of auxin signaling-related genes was significantly different, Similar results were observed for abscisic acid and jasmonic acid. These results indicate that LOC_Os04g43910 is mostly likely the target gene of qSE4, and the study of its gene function is of great significance for understanding the molecular mechanisms of SER and improving the efficiency of hybrid seed production. [ABSTRACT FROM AUTHOR]

The field pea has both semi-leafless (SL) and leafed (L) types. Mixing these two types together might improve yield by optimizing pea solar radiation interception, reducing lodging, and decreasing disease. However, an optimum mixing ratio has not yet been established, since previous studies mixed two leaf types from two separate varieties. This study used four near-isogenic pairs of pea genotypes differing only in leaf type to determine the optimal mixing ratio for yield and agronomic traits. Two leaf types were mixed at seeding in five mixing ratios: 0:100, 50:50, 67:33, 83:17, and 100:0 SL/L. With precise UAV quantification of canopy height (r2 = 0.88, RMSE = 2.6 cm), the results showed that a ratio of over 67% semi-leafless pea had a 10% greater lodging resistance when compared to the leafed monoculture. For mycosphaerella blight and Uromyce viciae-fabae rust diseases, the 83:17 mixture decreased disease severity by 4% when compared with the leafed monoculture. Regression analysis of yield estimated that the 86:14 ratio provided an 11% increase to the leafed monoculture, but there was no increase compared with the semi-leafless monoculture. Mixing the two types in a high semi-leafless ratio can reduce leafed lodging and prevent yield loss but does not increase the overall yield over the semi-leafless monoculture. [ABSTRACT FROM AUTHOR]

Grain weight (GW), one of the yield components of rice (Oryza sativa L.), is an important trait for improving rice productivity. In the 1990s, New Plant Type (NPT) rice breeding focused on improving the yield potential of rice varieties by introducing unique traits from Tropical Japonica Group cultivars. To reveal the genetic factors responsible for yield-related traits of NPT varieties, we previously developed 334 introgression lines with variations in traits inherited from NPT varieties in the genetic background of an Indica Group cultivar, 'IR 64'. Three of the NPT varieties—'IR65600-87-2-2-3', 'IR69093-41-2-3-2', and 'IR71195-AC1'—had heavier GW than 'IR 64'. To identify the genetic basis for the heavier GW in these lines, here we performed QTL analysis in F2 (BC4F2 equivalent) populations. We detected one each QTL for GW on chromosome 5 in the three populations, and developed three near-isogenic lines (NILs) with a QTL for GW, qGW5 (qGW5.1-YP1, qGW5.2-YP5, and qGW5.3-YP10), through marker-assisted selection. These three NILs were confirmed to have heavier GW than 'IR 64'. These NILs are useful materials in research and breeding for improvement of rice productivity. [ABSTRACT FROM AUTHOR]

Rice plants are affected by low-temperature stress during germination, vegetative growth, and reproductive stages. Thirty-nine rice genotypes including 36 near-isogenic lines (NILs) of BRRI dhan29 were evaluated to investigate the level of cold tolerance under artificially induced low temperature at the seedling stage. Three cold-related traits, leaf discolouration (LD), survivability, and recovery rate, were measured to determine the level of cold tolerance. Highly significant variation among the genotypes was observed for LD, survivability, and recovery rate. Three NILs, IR90688-74-1-1-1-1-1, IR90688-81-1-1-1-1-1, and IR90688-103-1-1-1-1-1, showed tolerance in all three traits, while IR90688-118-1-1-1-1-1 showed cold tolerance with LD and recovery rate. IR90688-92-1-1-1-1-1, IR90688-125-1-1-1-1-1, IR90688-104-1-1-1-1-1, IR90688-124-1-1-1-1-P2, IR90688-15-1-1-1-1-1, and IR90688-27-1-1-1-1-1 showed significantly higher yield coupled with short growth duration and good grain quality. Genetic analysis with SSRs markers revealed that the high-yielding NILs were genetically 67% similar to BRRI dhan28 and possessed cold tolerance at the seedling stage. These cold-tolerant NILs could be used as potential resources to broaden the genetic base of the breeding germplasm to develop high-yielding cold-tolerant rice varieties. [ABSTRACT FROM AUTHOR]

The development of crop varieties with high nitrogen-use efficiency (NUE) is thought to be important in achieving sustainable cereal crop production. The high yield large-grain rice cultivar Oryza sativa L. ‘Akita 63’ (temperate japonica) has high physiological NUE (PNUE) for grain yield (GY). Our previous study revealed that a large-grain allele of GS3 is present in ‘Akita 63’. Here, we verified the influence of GS3 on the yield properties and PNUE for GY in ‘Akita 63’. The frequency distribution of brown rice length in F2 crosses of ‘Iwate 75’ and ‘Akita 63’ showed a continuous distribution that could be explained by GS3. A near-isogenic line was developed to substitute the GS3 segment of ‘Koshihikari’, which harbours a normalsized grain allele, in the genetic background of ‘Akita 63’ and the line was designated as Akita63NILGS3- Koshihikari. Compared with Akita63NILGS3-Koshihikari, ‘Akita 63’ exhibited a significantly increased grain length, single brown grain weight and GY, although no significant differences were observed in the nitrogen content and above-ground biomass per unit of cultivated area. These results indicate that the GS3 large-grain allele is a contributing factor to high PNUE for GY in ‘Akita 63’. These findings will facilitate the development of nitrogen-efficient rice varieties. [ABSTRACT FROM AUTHOR]

Magnaporthe oryzae is known for its genetic diversity and pathogenic variability, leading to rapid breakdown of resistance in rice. Incorporating multiple broad-spectrum blast resistance genes into rice cultivars would extend disease resistance longevity. Effective resistance breeding in rice therefore requires continual enrichment of the reservoir of resistance genes and alleles. We conducted a large-scale screen of rice blast resistance in about 2 000 rice accessions. Among them, 247 accessions showed at least medium resistance to the natural infection of rice blast and 7 novel Pik alleles were identified from them. Variations in gene sequences were then correlated with the phenotypic trait to enable the identification of favorable alleles. Among the seven novel Pik alleles, the resistant rate of Pik-R0/ME/7017 donors was greater than 80%, and the disease score was less than 3. Through molecular marker-assisted backcross breeding, we successfully transferred the three Pik alleles, Pik-R0/ME/7017 , into an elite cultivated line Kongyu 131 to obtain BC 3 F 2 lines, which showed enhanced resistance to rice blast compared with the recurrent parent. Assessment of these near-isogenic lines in the greenhouse using 31 isolates of M. oryzae from Heilongjiang Province of China revealed that the resistant levels of the BC 3 F 2 lines with Pik-R0/ME/7017 were significantly higher than those of the established cloned resistance genes Pik-m and Pi1. Exploring such alleles will enrich our gene library for resistance to rice blast. [ABSTRACT FROM AUTHOR]

Abstract Background Male sterility (MS) has important applications in hybrid seed production, and the abortion of anthers has been observed in many plant species. While most studies have focused on the genetic factors affecting male sterility, the dynamic gene expression patterns of pollen abortion in male sterile lines have not been fully elucidated. In addition, there is still no hybrid oat that is commercially planted due to the lack of a suitable system of male sterility for hybrid breeding. Results In this study, we cultivated a male sterile oat line and a near-isogenic line by crossbreeding to elucidate the expression patterns of genes that may be involved in sterility. The first reported CA male sterile (CAMS) oat line was used for cross-testing and hybridization experiments and was confirmed to exhibit a type of nuclear sterility controlled by recessive genes. Oat stamens of two lines were sampled at four different developmental stages separately. Paired-end RNA sequencing was performed for each sample and generated 252.84 Gb sequences. There were 295,462 unigenes annotated in public databases in all samples, and we compared the histological characteristics and transcriptomes of oat stamens from the two oat lines at different developmental stages. Our results demonstrate that the sterility of the male sterile oat line occurs in the early stage of stamen development and is primarily attributable to abnormal meiosis and the excessive accumulation of superoxide. Conclusions To the best of our knowledge, this study is the first to decipher the dynamic expression profiles of pollen abortion CAMS and CA male fertile (CAMF) oat lines, which may represent a valuable resource for further studies attempting to understand pollen abortion and anther development in oats.

Abstract Background Chlorophyll is the most important factor enabling plants to absorb, transfer and transform light energy and plays an important role in yield formation. Brassica napus is one of the most important oil crops. Breeding Brassica napus for high light efficiency by improving photosynthetic efficiency has considerable social and economic value. In Brassica napus, there have been studies of the initial location of chlorophyll in seed embryos and pericarps, but there are few reports on the fine mapping of chlorophyll QTLs. We constructed near-isogenic lines (NIL), fine-mapped a chlorophyll locus, and evaluated the effect of this dominant locus on agronomic traits. Results The cqSPDA2 locus was mapped to an interval of 21.87–22.91 Mb on the chromosome A02 of Brassica napus using doubled haploid (DH) lines. To fine-map cqSPDA2, we built NIL and designed Indel primers covering the mapping interval. The 469 individuals in the BC3F2 population were analyzed using these indel primers. Among these indel primers, 15 could narrow the mapping interval to 188 kb between Indel3 and Indel15. Next, 16 indel primers and 19 SSR primers were designed within the new narrower mapping interval, and 5 of the primer-amplified fragments were found to be polymorphic and tightly linked to the cqSPDA2 locus in the BC4F2 population. The mapping interval was narrowed to 152 kb on A02 between SSR2 and Indel15. By gene expression analysis, we found three annotated genes in the mapping interval, including BnaA02g30260D, BnaA02g30290D and BnaA02g30310D, which may be responsible for chlorophyll synthesis. Conclusions The locus cqSPDA2, a dominant QTL for chlorophyll content in Brassica napus, was fine-mapped to a 21.89–22.04 Mb interval on A02. Three annotated genes (BnaA02g30260D, BnaA02g30290D and BnaA02g30310D) that may be responsible for chlorophyll synthesis were found.

Wheat blast caused by Pyricularia oryzae pathotype Triticum (MoT) has been transmitted from South America to Bangladesh and Zambia and is now spreading in these countries. To prepare against its further spread to Asian countries, we introduced Rmg8 , a gene for resistance to wheat blast, into a Japanese elite cultivar, Chikugoizumi (ChI), through recurrent backcrosses and established ChI near-isogenic lines, #2-1-10 with the Rmg8 / Rmg8 genotype and #4-2-10 with the rmg8 / rmg8 genotype. A molecular analysis suggested that at least 96.6% of the #2-1-10 genome was derived from the recurrent parent ChI. The #2-1-10 line was resistant to MoT not only in primary leaves at the seedling stage but also in spikes and flag leaves at the heading stage. The strength of the resistance in spikes of this Rmg8 carrier was comparable to that of a carrier of the 2NS segment, which has been the only genetic resource released to farmers' fields for wheat blast resistance. On the other hand, the 2NS resistance was not expressed on leaves at the seedling stage nor flag leaves at the heading stage. Considering that leaf blast has been increasingly reported and regarded as an important inoculum source for spike blast, Rmg8 expressed at both the seedling and heading stages, or more strictly in both leaves and spikes, is suggested to be useful to prevent the spread of MoT in Asia and Africa., Competing Interests: The author(s) declare no conflict of interest.

Brown spot (BS) caused by Bipolaris oryzae is a serious disease of rice and decreases grain yield. Breeding for BS resistance is an economical solution but has not hitherto been achieved. To develop a practical BSresistant variety, we introduced a chromosomal segment including a quantitative trait locus (QTL) for BS resistance, qBSfR11, derived from the BS-resistant local resource 'Tadukan', into the genetic background of the high-yielding but susceptible 'Mienoyume'. Resistance is controlled by a single recessive gene in a 1.3-Mbp region. We named this gene bsr1 (brown spot resistance 1). The near-isogenic line bsr1-NIL had a greater yield with larger grain width than Mienoyume but similar other agronomic traits in fields where BS was mild; it had a significantly lower BS disease score and a 28.8% higher yield in fields where BS was more severe, and it showed resistance to multiple isolates of BS fungus. It showed stable resistance to BS and had excellent agricultural traits in the presence of BS. We developed the bsr1-NIL with resistance to BS and applied it for variety registration to Ministry of Agriculture, Forestry and Fisheries in Japan as 'Mienoyume BSL'. This is the first report for the BS resistant rice variety bred using marker-assisted selection. [ABSTRACT FROM AUTHOR]

Phosphorus, essential for growth/productivity of plants, is acquired through roots in the form of inorganic phosphate (Pi). The molecular mechanism of low Pi tolerance in plants is still not fully understood. Functions of Pup1 QTL in Pi-deficiency tolerance in rice are sparsely understood. To decipher the molecular functions of qPup1 in Pi-homeostasis in rice, integrated transcriptome-proteome analysis of contrasting rice genotypes grown under Pi-starvation stress was performed. Our integrated analysis identified 4614 transcripts and 107 proteins differentially expressed in roots of NIL-23 (Pi-deficiency tolerant, harboring qPup1), whereas 8555 transcripts and 687 proteins were differentially expressed in shoots of NIL-23 under Pi-starvation stress. The integrated analysis indicated 146 transcripts/proteins expressed in shoots, while 18 transcripts/proteins expressed in roots of NIL-23, which might be responsible for making it stress resilient. The genes/proteins for TFs, P metabolism, starch/sucrose metabolism, and RNA-mediated post-transcriptional regulation play important roles in Pi-starvation in rice. Functional annotation of differentially transcribed genes/expressed proteins indicated transcription factors, phosphorus/starch/sucrose metabolism, and RNA-mediated post-transcriptional regulation to be important players in Pi-starvation resilience of NIL-23. Up-regulated expression of genes/proteins under stress due to introgression of qPup1 deciphered regulatory functions of the QTL and the genes/proteins involved. These might help developing rice cultivar with improved P acquisition/use-efficiency for better performance in P-deficient soils. • Integrated transcriptome−proteome analysis revealed regulatory role of Pup1 QTL under P-starvation stress in rice. • Our analysis indicated 146 transcripts/proteins co-expressed in shoot, while 18 in root of NIL-23 making it stress-resilient. • Expression of genes/proteins for TFs, Pi/sugar metabolism, and post-transcriptional regulation played important roles. • Up-regulation of genes/proteins due to Pup1 QTL, particularly in leaf, plays important roles in stress tolerance. [ABSTRACT FROM AUTHOR]

Abstract Background Fusarium crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. A putative quantitative trait locus conferring FCR resistance, Qcrs.cpi-1H, had previously been mapped on the long arm of chromosome 1H in barley. Results In this study, five pairs of near-isogenic lines (NILs) targeting the 1HL locus were developed. Analysing the NILs found that the resistant allele at Qcrs.cpi-1H significantly reduced FCR severity. Transcriptomic analysis was then conducted against three of the NIL pairs, which placed the Qcrs.cpi-1H locus in an interval spanning about 11 Mbp. A total of 56 expressed genes bearing single nucleotide polymorphisms (SNPs) were detected in this interval. Five of them contain non-synonymous SNPs. These results would facilitate detailed mapping as well as cloning gene(s) underlying the resistance locus. Conclusion NILs developed in this study and the transcriptomic sequences obtained from them did not only allow the validation of the resistance locus Qcrs.cpi-1H and the identification of candidate genes underlying its resistance, they also allowed the delineation of the resistance locus and the development of SNPs markers which formed a solid base for detailed mapping as well as cloning gene(s) underlying the locus.

Abstract Background Leaf shape development research is important because leaf shapes such as moderate curling can help to improve light energy utilization efficiency. Leaf growth and development includes initiation of the leaf primordia and polar differentiation of the proximal-distal, adaxial-abaxial, and centrolateral axes. Changes in leaf adaxial-abaxial polarity formation, auxin synthesis and signaling pathways, and development of sclerenchyma and cuticle can cause abnormal leaf shapes such as up-curling leaf. Although many genes related to leaf shape development have been reported, the detailed mechanism of leaf development is still unclear. Here, we report an up-curling leaf mutant plant from our Brassica napus germplasm. We studied its inheritance, mapped the up-curling leaf locus BnUC1, built near-isogenic lines for the Bnuc1 mutant, and evaluated the effect of the dominant leaf curl locus on leaf photosynthetic efficiency and agronomic traits. Results The up-curling trait was controlled by one dominant locus in a progeny population derived from NJAU5734 and Zhongshuang 11 (ZS11). This BnUC1 locus was mapped in an interval of 2732.549 kb on the A05 chromosome of B. napus using Illumina Brassica 60 K Bead Chip Array. To fine map BnUC1, we designed 201 simple sequence repeat (SSR) primers covering the mapping interval. Among them, 16 polymorphic primers that narrowed the mapping interval to 54.8 kb were detected using a BC6F2 family population with 654 individuals. We found six annotated genes in the mapping interval using the B. napus reference genome, including BnaA05g18250D and BnaA05g18290D, which bioinformatics and gene expression analyses predicted may be responsible for leaf up-curling. The up-curling leaf trait had negative effects on the agronomic traits of 30 randomly selected individuals from the BC6F2 population. The near-isogenic line of the up-curling leaf (ZS11-UC1) was constructed to evaluate the effect of BnUC1 on photosynthetic efficiency. The results indicated that the up-curling leaf trait locus was beneficial to improve the photosynthetic efficiency. Conclusions An up-curling leaf mutant Bnuc1 was controlled by one dominant locus BnUC1. This locus had positive effects on photosynthetic efficiency, negative effects on some agronomic traits, and may help to increase planting density in B. napus.

Wheat (Triticum aestivum L.) grain yield is predicted to decrease in the future because of an increase in air temperature globally. To clarify the effects of the vernalization response gene in wheat to warmer winters, we compared dry matter production and grain yield between spring wheat ‘Asakazekomugi’ and its winter-type near-isogenic line (NIL) carrying different alleles of the vernalization response gene Vrn-D1 under early-, standard-, and late-sowing conditions. Under early-sowing conditions, dry matter production of the NIL carrying the winter allele of Vrn-D1, named Asa (Vrn-D1b), exceeded that of ‘Asakazekomugi’ from mid-March (after stem elongation in Asa (Vrn-D1b)) when the temperatures rose. Tiller number and leaf area index under early-sowing conditions were consistently higher in Asa (Vrn-D1b) than in ‘Asakazekomugi’ from mid-March onward. It was suggested that the early-sown ‘Asakazekomugi’ could not effectively absorb solar radiation to produce dry matter because of the acceleration of stem elongation caused by the Vrn-D1 gene during the cold season. The grain yield of Asa (Vrn-D1b) with early sowing was higher than with standard sowing. In contrast, the grain yield of ‘Asakazekomugi’ was lower in the early-sown crop than in the crop sown at the standard date. These results suggested that the higher grain yield of Asa (Vrn-D1b) than that of ‘Asakazekomugi’ under early-sown conditions could be due to Asa (Vrn-D1b) maintaining high dry matter production after the jointing stage by suppressing acceleration of growth caused by warm conditions after sowing. Abbreviations CGR: crop growth rate; HI: harvest index; LAI: leaf area index; NIL: near-isogenic line; SNP: single-nucleotide polymorphism

Abstract Background Although rapeseed (Brassica napus L.) mutant forming multiple siliques was morphologically described and considered to increase the silique number per plant, an important agronomic trait in this crop, the molecular mechanism underlying this beneficial trait remains unclear. Here, we combined bulked-segregant analysis (BSA) and whole genome re-sequencing (WGR) to map the genomic regions responsible for the multi-silique trait using two pools of DNA from the near-isogenic lines (NILs) zws-ms (multi-silique) and zws-217 (single-silique). We used the Euclidean Distance (ED) to identify genomic regions associated with this trait based on both SNPs and InDels. We also conducted transcriptome sequencing to identify differentially expressed genes (DEGs) between zws-ms and zws-217. Results Genetic analysis using the ED algorithm identified three SNP- and two InDel-associated regions for the multi-silique trait. Two highly overlapped parts of the SNP- and InDel-associated regions were identified as important intersecting regions, which are located on chromosomes A09 and C08, respectively, including 2044 genes in 10.20-MB length totally. Transcriptome sequencing revealed 129 DEGs between zws-ms and zws-217 in buds, including 39 DEGs located in the two abovementioned associated regions. We identified candidate genes involved in multi-silique formation in rapeseed based on the results of functional annotation. Conclusions This study identified the genomic regions and candidate genes related to the multi-silique trait in rapeseed.

Soil salinity is a major constraint to sustainable crop production. Genetic improvements are needed for growing soybean in salinity-prone environments. Salt-tolerant soybean genotypes alleviate a reduction in photosynthesis and growth under saline conditions; however, the detailed mechanisms involved remain unclear. Here, we aimed to clarify how Na and Cl root-to-leaf transport is quantitatively regulated, and to identify whether photosynthetic tolerance depends on traits associated with either stomata or with mesophyll tissues. Two pairs of pot-grown soybean near-isogenic lines (NILs) consisting of tolerant and susceptible counterparts, derived from a cross between salt-tolerant FT-Abyara and salt-sensitive C01, were subjected to salinity treatment in a rainout greenhouse. Comparison of photosynthetic responses between genotypes indicated that genotypic differences in salinity tolerance depended on the ability for sustained CO2 assimilation in mesophyll tissues, rather than stomatal conductance. The ratio of photosynthetic rate to intercellular CO2 concentration (A/Ci) declined exponentially with increasing Na and Cl concentration regardless of genotype, but tolerant genotypes effectively kept both elements at significantly low levels. Under saline conditions, tolerant genotypes reduced Na and Cl content at the two transport pathways: from root to stem, and from stem to leaf, but the reduction of Cl at each pathway was only minor. These results suggest that integrating genetic capacity for Cl transport regulation and osmotic adjustment should be an important target in salinity-tolerance soybean breeding.

The field pea has both semi-leafless (SL) and leafed (L) types. Mixing these two types together might improve yield by optimizing pea solar radiation interception, reducing lodging, and decreasing disease. However, an optimum mixing ratio has not yet been established, since previous studies mixed two leaf types from two separate varieties. This study used four near-isogenic pairs of pea genotypes differing only in leaf type to determine the optimal mixing ratio for yield and agronomic traits. Two leaf types were mixed at seeding in five mixing ratios: 0:100, 50:50, 67:33, 83:17, and 100:0 SL/L. With precise UAV quantification of canopy height (r2 = 0.88, RMSE = 2.6 cm), the results showed that a ratio of over 67% semi-leafless pea had a 10% greater lodging resistance when compared to the leafed monoculture. For mycosphaerella blight and Uromyce viciae-fabae rust diseases, the 83:17 mixture decreased disease severity by 4% when compared with the leafed monoculture. Regression analysis of yield estimated that the 86:14 ratio provided an 11% increase to the leafed monoculture, but there was no increase compared with the semi-leafless monoculture. Mixing the two types in a high semi-leafless ratio can reduce leafed lodging and prevent yield loss but does not increase the overall yield over the semi-leafless monoculture.

We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar 'Hwaseong' and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9 , which encodes an l -ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9- overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9 HS) and O. rufipogon (APX9 OR) alleles. indica accessions shared both alleles, suggesting that APX9 HS was introgressed into indica followed by crossing. The finding that O. rufipogon accessions with different origins carry APX9 OR suggests that the 3 bp insertion was specifically selected in japonica during its domestication. Our findings demonstrate that APX9 acts as a major regulator of plant development by controlling a valuable suite of agronomically important traits in rice. [ABSTRACT FROM AUTHOR]

BACKGROUND: Plutella xylostella has developed resistance to a variety of pesticides in the field. Selection, inheritance, a near‐isogenic line, cross‐resistance and biochemical mechanisms of pyridalyl resistance were characterized in a field‐collected resistant population of P. xylostella from China. RESULTS: Compared with a susceptible IVF‐S strain, the field‐collected FZ population showed ~ 350‐fold resistance to pyridalyl. The FZ‐PY strain, selected from the FZ population using pyridalyl, developed ~ 640‐fold resistance to pyridalyl. Inheritance tests indicated that pyridalyl resistance in the FZ‐PY strain was autosomal and incompletely recessive. Through successive backcrossing to IVF‐S, a near‐isogenic strain (NIL‐PY) was established that exhibited 191.21‐fold resistance to pyridalyl and no cross‐resistance to other tested popular insecticides. No significant effects of synergists and higher activities of metabolic enzymes were observed in NIL‐PY compared with IVF‐S. Furthermore, the survival rate of NIL‐PY larvae, and female oviposition, fecundity and egg viability were markedly reduced in NIL‐PY compared with IVF‐S. The fitness of NIL‐PY was found to be 0.56 compared with IVF‐S. CONCLUSION: Considering that no relevant effects of synergists or oxidative metabolism were observed in NIL‐PY, and that pyridalyl resistance results in significant fitness costs compared with IVF‐S, further research will be conducted on the mechanism of target‐site resistance. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Increasing incidence of chronic diseases in the 21st century has emphasized the importance of developing crops with enhanced nutritional value. Plant-based diets are associated with reduced incidence of many chronic diseases. The growing population and increased food demand have prioritized the development of high-yielding commercial crop varieties at the expense of natural flavors as well as health-benefiting compounds including polyphenols. Flavonoids are a large subfamily of polyphenols abundant in the plant kingdom with known health-promoting effects, making them a promising trait to be re-introduced into elite lines. Given the vast array of flavonoids and the complexity of plant food metabolome interactions, it is difficult to identify with certainty the specific class(es) of flavonoids in the food matrix that are anti-inflammatory. To address this, we have developed four maize near-isogenic lines (NILs); a line that lacked both anthocyanins and phlobaphenes, a second NIL containing phlobaphenes, a third line had anthocyanins, and a fourth line that contained both anthocyanins and phlobaphenes. The phytochemical profiles and the antioxidant potential of the NILs were characterized. The accumulation of anthocyanins and phlobaphenes contributed significantly to antioxidant capacity compared to maize lines that lacked one or both of the compounds (p < 0.05). Pilot study showed that intake of flavonoid-rich maize diets were able to alleviate experimental colitis in mice. These NILs offer novel materials combining anthocyanins and phlobaphenes and can be used as powerful tools to investigate the disease-preventive effects of specific flavonoid compound in diet/feeding experiments.

Background: Male sterility (MS) has important applications in hybrid seed production, and the abortion of anthers has been observed in many plant species. While most studies have focused on the genetic factors affecting male sterility, the dynamic gene expression patterns of pollen abortion in male sterile lines have not been fully elucidated. In addition, there is still no hybrid oat that is commercially planted due to the lack of a suitable system of male sterility for hybrid breeding. Results: In this study, we cultivated a male sterile oat line and a near-isogenic line by crossbreeding to elucidate the expression patterns of genes that may be involved in sterility. The first reported CA male sterile (CAMS) oat line was used for cross-testing and hybridization experiments and was confirmed to exhibit a type of nuclear sterility controlled by recessive genes. Oat stamens of two lines were sampled at four different developmental stages separately. Paired-end RNA sequencing was performed for each sample and generated 252.84 Gb sequences. There were 295,462 unigenes annotated in public databases in all samples, and we compared the histological characteristics and transcriptomes of oat stamens from the two oat lines at different developmental stages. Our results demonstrate that the sterility of the male sterile oat line occurs in the early stage of stamen development and is primarily attributable to abnormal meiosis and the excessive accumulation of superoxide. Conclusions: To the best of our knowledge, this study is the first to decipher the dynamic expression profiles of pollen abortion CAMS and CA male fertile (CAMF) oat lines, which may represent a valuable resource for further studies attempting to understand pollen abortion and anther development in oats. [ABSTRACT FROM AUTHOR]

Increasing incidence of chronic diseases in the 21st century has emphasized the importance of developing crops with enhanced nutritional value. Plant-based diets are associated with reduced incidence of many chronic diseases. The growing population and increased food demand have prioritized the development of high-yielding commercial crop varieties at the expense of natural flavors as well as health-benefiting compounds including polyphenols. Flavonoids are a large subfamily of polyphenols abundant in the plant kingdom with known health-promoting effects, making them a promising trait to be re-introduced into elite lines. Given the vast array of flavonoids and the complexity of plant food metabolome interactions, it is difficult to identify with certainty the specific class(es) of flavonoids in the food matrix that are anti-inflammatory. To address this, we have developed four maize near-isogenic lines (NILs); a line that lacked both anthocyanins and phlobaphenes, a second NIL containing phlobaphenes, a third line had anthocyanins, and a fourth line that contained both anthocyanins and phlobaphenes. The phytochemical profiles and the antioxidant potential of the NILs were characterized. The accumulation of anthocyanins and phlobaphenes contributed significantly to antioxidant capacity compared to maize lines that lacked one or both of the compounds (p < 0.05). Pilot study showed that intake of flavonoid-rich maize diets were able to alleviate experimental colitis in mice. These NILs offer novel materials combining anthocyanins and phlobaphenes and can be used as powerful tools to investigate the disease-preventive effects of specific flavonoid compound in diet/feeding experiments. [ABSTRACT FROM AUTHOR]

Background: Association mapping has been advocated as the method of choice for identifying loci involved in the inheritance of complex traits in crop species. This method involves identifying markers with significant differences in allele frequency between individuals with a phenotype of interest and a set of unrelated control individuals. Objective: The purpose of our study is not only to investigate the genetic diversity and relationships of the basic molecular markers of near-isogenic lines (NILs) of waxy maize, but it is also to identify molecular markers related to interesting seed characteristics including 4 seed quantity traits and 4 seed phenotypic traits using association analysis with population structure. Methods: We performed association mapping of 200 SSR markers and 8 seed characteristics among 10 NILs of waxy maize and two parental lines (HW3, HW9) (recurrent parent) of "Mibaek 2" variety. Results: In population structure and cluster analysis, the 10 NILs and two parental lines were divided into two groups. Seven inbred lines, including HW3, were assigned to Group I. Group II contained 5 inbred lines, including HW9. In addition, we found that 32 SSR markers associate with 8 seed characteristics in 10 NILs. In particular, five SSR markers (umc1986, umc1747, umc2275, phi078, umc1366) were together associated with more than one seed characteristics such as EL, 100 KW, SCC, R, L*, and V. Conclusion: This study demonstrated the utility of SSR analysis for studying GD, population structure, and association mapping in 10 NILs and two parental lines (HW3, HW9) of "Mibaek 2" variety. [ABSTRACT FROM AUTHOR]

Bacterial spot caused by several species of Xanthomonas is a devastating disease resulting in severe fruit yield loss and quality decline in tomato production areas worldwide. Lack of resistant commercial varieties is among the most critical factors limiting the application of integrated management to control the disease. Although sources for resistance to all species and races have been discovered over years, breeding for resistance to the disease is slow because the resistance is quantitatively inherited and sometimes linked to poor horticultural traits. Development of near-isogenic lines (NILs) by introgressing the shortest DNA fragment of the resistance gene region from the donor into elite cultivars is a promising approach to eliminating the negative effect on horticultural traits. In the current study, a strategy of combining traditional backcross with molecular marker-assisted foreground and background selection was adopted to generate NILs carrying the Rx4 gene for resistance to Xanthomonas euvesicatoria pv. perforans race T3 strain. The donor parent is a wild species Solanum pimpinellifolium accession PI 128216, and the recurrent parent is an elite processing tomato breeding line OH88119. Disease evaluation was performed in F1, BC4F1, BC6F1, BC6F2, BC6F3, and BC6F4 generations by infiltration of race T3 strain Xv829 to leaves of plants. Meanwhile, fruit traits including fruit weight, fruit color parameters, soluble solid content, pH, and firmness were collected from replicated field trials in BC6F4 and BC6F5. Five NILs with 159–1901 kb DNA fragments in the Rx4 gene region were obtained. They all showed high level of hypersensitive resistance to race T3, and their fruit traits were not significantly different from the recurrent parent OH88119. However, fruit weight of one NIL Rx4–1812 carrying the largest DNA fragment of 1901 kb in the Rx4 gene region was 9.5–11.8% lower than OH8819 though the difference was not statistically significant. This might be due to the linkage drag of FW11.2, a QTL for fruit weight in the same region. Overall, the NILs created here can be used as sources for developing resistant varieties and deciphering the mechanism of resistance to bacterial spot in tomato. [ABSTRACT FROM AUTHOR]

Seed coat cracking in soybeans [Glycine max (L). Merr.] leads to commercial and agronomic losses. The Japanese elite soybean cultivar 'Fukuyutaka' is often used as a parent for breeding, but its high rate of seed coat cracking is an obstacle to its further use in breeding programs. To establish a DNA marker-assisted selection system for seed coat cracking, genetic factors related to high rates of seed coat cracking were surveyed, and a quantitative trait locus (QTL) with a stable effect on seed coat cracking in both years of a two-year replication experiment was detected on chromosome 20. Comparison of a set of near-isogenic lines (NILs) around this locus verified that the presence of the 'Fukuyutaka' allele significantly increased seed coat cracking in the kernel. The locus is located in a genomic region spanning 3.2 Mb. Marker-assisted selection for the locus will improve the selection efficiency of 'Fukuyutaka'-derived breeding populations. [ABSTRACT FROM AUTHOR]

Identifying important regulative elements and pathways related to dwarfism in cotton is a major challenge in cotton breeding. Isobaric tags for relative and absolute quantitation-based proteomics of stem terminal buds from upland cotton (Gossypium hirsutum L.) dwarf line LA-1 and high near-isogenic line LH-1 was performed. Moreover, transcriptional expression of differentially-expressed proteins (DEPs) belonging to phytohormone signal transduction, hormone biosynthesis, and ubiquitin system were analysed using quantitative real-time polymerase chain reaction. A total of 4 849 proteins were identified from LA-1 and LH-1, 697 of which showed differential accumulations. Most of the DEPs have catalytic, binding, and transporter activity and are involved in metabolism- and protein processing-related pathways. In particular, seven DEPs, including two gibberellin (GA) receptors, three cytokinin (CK) receptors, CKoxidase, and CK-N-glucosyltransferase were up-regulated in LA-1, and GA20-oxidase was down-regulated in LH-1. Our results suggest that the DELLA-independent GAsignalling pathway is the primary cause of dwarfism in LA-1 and indicate that CKresponse element 1-2, GA-insensitive dwarf, CKoxidase, and GA3-β-dioxygenase are potential indicators of dwarf cotton. The profiling of DEPs may offer a valuable resource for cotton breeding.

The fruit flesh of watermelons differs depending on the distinct carotenoid composition. Orange-colored flesh relates to the accumulation of β-carotene, which is beneficial to human health. Canary-yellow-fleshed OTO-DAH and orange-β-fleshed (orange-fleshed with high β-carotene) NB-DAH near-isogenic lines (NILs) were used to determine the genetic mechanism attributed to orange watermelon flesh. For genetic mapping, an F 2 population was developed by crossing the two NILs. The segregation ratio of flesh color in the F 2 population indicated that the orange-β flesh of the NB-DAH NIL was controlled by a single incompletely dominant gene. Through a comparative analysis of the whole-genome sequences of the parent lines and NILs, a major introgression region unique to the NB-DAH NIL was detected on Chr. 1; this was considered a candidate region for harboring genes that distinguish orange from canary-yellow and red flesh. Among the 13 genes involved in the carotenoid metabolic pathway in watermelons, only ClPSY1 ( ClCG01G008470 ), which encodes phytoene synthase 1, was located within the introgression region. The genotyping of F 2 plants using a cleaved amplified polymorphic sequence marker developed from a non-synonymous SNP in ClPSY1 revealed its relationship with orange-β flesh. The insights gained in this study can be applied to marker-assisted breeding for this desirable trait.

It is reported that the absence of lipoxygenase-3 (LOX-3) may contribute to a reduction in stale flavor after the storage of rice. To improve the quality of stored rice of the Korean japonica rice cultivar, we conducted a breeding program to develop near-isogenic rice without LOX-3 in the genetic background of Saenuri, a mega variety of Korea. In the first step of the breeding program, we used a donor parent of LOX-3 null, Daw Dam, and a recurrent japonica parent, Sindongjin, to develop HR27873-AC12 by backcross (BC1), color test for introgression of lox-3, and anther culture for rapid fixation. In the second step, we used the donor parent, HR27873-AC12, and the recurrent parent, Saenuri, to develop HR28896-31-3-1-1 by backcross (BC1), marker-assisted selection (MAS) for lox-3, and phenotypic selection (PS) for agronomic traits. Finally, in the third step, we developed HR30960-186-2-1-2-1 (Jeonju624), derived from a cross between Saenuri and HR28896-31-3-1-1, by MAS for lox-3 and PS with high selection pressure for agronomic characteristics. Jeonju624 was confirmed with the introgression of lox-3 by molecular marker. Jeonju624 was a mid-late maturing rice with similar agronomic characteristics to Saenuri, lodging tolerance with short culm, erect plant architecture, and resistance to bacterial blight and rice stripe virus. The yield components of Jeonju624 were mostly similar to Saenuri, except for the 1,000-grain weight of brown rice. The appearance of the grain of Jeonju624 was better than that of Saenuri, and the characteristics of cooked rice were similar to those of Saenuri. In the genetic background analysis using 406 KASP (Kompetitive Allele-Specific PCR) markers, Jeonju624 was confirmed to be the near-isogenic line (NIL) of Saenuri with a 95.8% recovery rate. Jeonju624 is the NIL of Saenuri without LOX-3, and overcomes the linkage drag of Daw Dam with similar agronomic characteristics and genetic background to Saenuri. Jeonju624 can be utilized as a practical cultivar to improve the quality of stored rice, breeding material for the introgression of lox-3, and genetic material to elucidate the effect of introgressed genes. [ABSTRACT FROM AUTHOR]

Wheat (Triticum aestivum L.) grain yield is predicted to decrease in the future because of an increase in air temperature globally. To clarify the effects of the vernalization response gene in wheat to warmer winters, we compared dry matter production and grain yield between spring wheat 'Asakazekomugi' and its winter-type near-isogenic line (NIL) carrying different alleles of the vernalization response gene Vrn-D1 under early-, standard-, and late-sowing conditions. Under early-sowing conditions, dry matter production of the NIL carrying the winter allele of Vrn-D1, named Asa (Vrn-D1b), exceeded that of 'Asakazekomugi' from mid-March (after stem elongation in Asa (Vrn-D1b)) when the temperatures rose. Tiller number and leaf area index under early-sowing conditions were consistently higher in Asa (Vrn-D1b) than in 'Asakazekomugi' from mid-March onward. It was suggested that the early-sown 'Asakazekomugi' could not effectively absorb solar radiation to produce dry matter because of the acceleration of stem elongation caused by the Vrn-D1 gene during the cold season. The grain yield of Asa (Vrn-D1b) with early sowing was higher than with standard sowing. In contrast, the grain yield of 'Asakazekomugi' was lower in the early-sown crop than in the crop sown at the standard date. These results suggested that the higher grain yield of Asa (Vrn-D1b) than that of 'Asakazekomugi' under early-sown conditions could be due to Asa (Vrn-D1b) maintaining high dry matter production after the jointing stage by suppressing acceleration of growth caused by warm conditions after sowing. Abbreviations: CGR: crop growth rate; HI: harvest index; LAI: leaf area index; NIL: near-isogenic line; SNP: single-nucleotide polymorphism [ABSTRACT FROM AUTHOR]

Soil salinity is a major constraint to sustainable crop production. Genetic improvements are needed for growing soybean in salinity-prone environments. Salt-tolerant soybean genotypes alleviate a reduction in photosynthesis and growth under saline conditions; however, the detailed mechanisms involved remain unclear. Here, we aimed to clarify how Na and Cl root-to-leaf transport is quantitatively regulated, and to identify whether photosynthetic tolerance depends on traits associated with either stomata or with mesophyll tissues. Two pairs of pot-grown soybean near-isogenic lines (NILs) consisting of tolerant and susceptible counterparts, derived from a cross between salt-tolerant FT-Abyara and salt-sensitive C01, were subjected to salinity treatment in a rainout greenhouse. Comparison of photosynthetic responses between genotypes indicated that genotypic differences in salinity tolerance depended on the ability for sustained CO2 assimilation in mesophyll tissues, rather than stomatal conductance. The ratio of photosynthetic rate to intercellular CO2 concentration (A/Ci) declined exponentially with increasing Na and Cl concentration regardless of genotype, but tolerant genotypes effectively kept both elements at significantly low levels. Under saline conditions, tolerant genotypes reduced Na and Cl content at the two transport pathways: from root to stem, and from stem to leaf, but the reduction of Cl at each pathway was only minor. These results suggest that integrating genetic capacity for Cl transport regulation and osmotic adjustment should be an important target in salinity-tolerance soybean breeding. [ABSTRACT FROM AUTHOR]

Manipulating the genetic control of plant height is essential in soybean breeding to increase yield through the enlargement of the plant size while preventing lodging. A Japanese soybean germplasm, Y2, has distinctively shorter inter-node lengths than those of recently developed Japanese cultivars and is expected to provide new variation to prevent lodging. A quantitative trait loci (QTL) analysis for plant height-related traits was conducted using F2 individuals derived from a cross between the elite Japanese cultivar Fukuyutaka and Y2. A major QTL for average inter-node length (AIL) and plant height was identified on chromosome 13 and named qSI13-1 (QTL for short inter-node on chromosome 13). The Y2 allele of qSI13-1 was partially dominant for plant height. qSI13-1 exhibited no effect on either days to flowering or number of main stem nodes. The AILs and plant heights of the near-isogenic lines containing the Y2 allele of qSI13-1 in the genetic background of Fukuyutaka were significantly less than those of Fukuyutaka. No significant differences between the near-isogenic lines and Fukuyutaka were observed for seed yield and flowering date, indicating that qSI13-1 will be useful in developing cultivars with short plant heights without having negative effects on yield potential and days to flowering. [ABSTRACT FROM AUTHOR]

Near-isogenic lines (NILs), carrying different combinations of Ppd-1 genes in the genetic background of an early-maturity cultivar Abukumawase were grown at two sites for two years to elucidate the effects of photoperiodic response genes on the growth and yield of early-maturity wheat ( Triticum aestivum L.) in central and southwestern Japan. Photoperiod-insensitive genes, Ppd-B1a and Ppd-D1a , accelerated young spike development, and this effect was predominant with Ppd-B1 with no additive effect among them. Ppd-B1a and Ppd-D1a also advanced the jointing stage, heading, and maturity, and the effect of Ppd-B1a on the jointing stage and heading was stronger than that of Ppd-D1a. An additive effect of two genes was detected for heading. Besides, Ppd-B1a and Ppd-D1a reduced culm length and grain weight, although the reduction effect on grain weight was not significant. Meanwhile, the mean temperature from double ridge formation stage to heading was lower in NILs with photoperiod-insensitive genes than in NILs with photoperiod-sensitive gene, and there was a significant correlation between mean temperature from double ridge formation stage to terminal spikelet formation stage and spikelet number per spike as well as between mean temperature from terminal spikelet formation stage to heading and grain number per spikelet. Therefore in a genetic background of extremely early-maturity line of spring type wheat, photoperiod-insensitive genes accelerated wheat growth and reduced spikelet numbers in central and southwestern Japan, and the effect of Ppd-B1a was stronger than that of Ppd-D1a.

Background and objectives: Near‐isogenic lines (NILs) of three Chinese winter wheat varieties were used to explore quality differences between subunits 5 + 10 and 2 + 12. Protein content, gluten quality, rheological properties, and bread‐making quality in the NILs possessing subunits 5 + 10 and 2 + 12 were assessed and compared. Findings: All measured parameters except protein content significantly changed when subunits 2 + 12 were replaced by subunits 5 + 10. The incorporation of subunits 5 + 10, in the absence of subunits 2 + 12, increased dramatically dough strength, but the extensibility was slightly decreased. The improved functionality of subunits 5 + 10 was only pronounced in the recipient cultivar (Xiaoyan 22) which had weak gluten strength but better extensibility, whereas, the inferior overall quality was obtained in the recipient cultivars (Xinong 2208 and Xinong 1718) carrying medium‐to‐strong gluten strength and poor extensibility. Conclusions: The functionality of subunits 5 + 10 was well expressed in the recipient cultivars with weak gluten strength and better extensibility. Significance and novelty: The findings expanded our knowledge on the functionality of subunits 5 + 10 on different genetic backgrounds with gradient elasticity‐to‐extensibility ratio. The transformed lines with extremely strong gluten strength and reduced extensibility could be used as parents in wheat quality breeding and their flour would be suitable for blending with flour of the lower grade. [ABSTRACT FROM AUTHOR]

Abstract: Mapping and isolation of quantitative trait loci (QTLs) or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding. To identify the QTLs controlling grain size and weight, we developed a near isogenic line F 2 (NIL-F 2 ) population, which was derived from a residual heterozygous plant in an F 7 generation of recombinant inbred line (RIL). With the completion of more than 30ÿ whole genome re-sequencing of the parents, two DNA bulks for large and small grains, a total of 58.94 Gb clean nucleotide data were generated. A total of 455 262 single nucleotide polymorphisms (SNPs) between the parents were identified to perform bulked QTL-seq. A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5. We designated the major QTL in the candidate region as qTGW5.3 . Then, qTGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F 2 population. Furthermore, recombinants and the progeny tests delimited the candidate region of qTGW5.3 to 1.13 Mb, flanked by HX5009 (15.15 Mb) and HX5003 (16.28 Mb). A set of NILs, selected from the F 2 population, was developed to evaluate the genetic effect of qTGW5.3 . Significant QTL effects were detected on grain length, grain width and 1000-grain weight of H12-29 allele with 1.14 mm, -0.11 mm and 3.11 g, which explained 99.64%, 95.51% and 97.32% of the phenotypic variations, respectively. [ABSTRACT FROM AUTHOR]