Appearance Quality Traits Research Articles

Genome-wide association study of appearance quality traits and development of KASP makers in vegetable soybean

Vegetable soybean [(Glycine max (L.) Merr.], commonly referred to as edamame, holds significant agricultural importance in China as a legume vegetable harvested at the pod-filling stage (R6). The visual appeal of vegetable soybeans, crucial for consumer preference and marketability, depends on factors such as pod length, pod width, and pod color. This study cultivated 264 vegetable soybeans in Nanjing, Huai'an, and Nantong to assess pod traits using PlantPhenoM, a system for pod phenotypic identification and analysis. Results revealed a variability range of 8.64 to 30.00% in appearance quality traits among vegetable soybeans. Leveraging phenotypic data and employing a genome-wide association study (GWAS) we identified 525 SNPs significantly linked to appearance quality traits in different regions. In addition, candidate genes (Glyma.04G004700, Glyma.15G051600, Glyma.18G225700, Glyma.18G225900, and Glyma.18G272300) associated with target traits were identified, and KASP markers for S04_372771 (pod length), S18_51477324 (pod width), and S18_55553200 (pod color) were developed, respectively. This research offers valuable insights for breeding superior vegetable soybean varieties and lays the groundwork for exploring candidate genes and molecular markers related to appearance and quality traits in vegetable soybeans.

OsAAP3 Gene Mutation Promotes the Chalkiness Character in Rice

Rice chalkiness is one of the most important appearance quality traits and has a great impact on its processing quality, nutritional quality, cooking, and eating quality traits. It has important theoretical significance and application value to clarify the genetic mechanism of rice chalkiness. To reveal the relationship between chalkiness of OsAAP3 mutant rice and the shape, structure and arrangement of endosperm cells and starch grains, which will lay a foundation for further research on the formation mechanism of chalkiness character of rice and the cultivation of new high-quality rice varieties. The results showed that the chalkiness, chalkiness rate, and chalkiness area of OsAAP3 mutant rice significantly increased compared with the control ZH11, and there were significant variations in the arrangement, morphology, and cross-section starch grain distribution of the endosperm cells of the mutant rice: the white heart area of the mutant increased, and the white belly almost distributed in the edge of the whole rice cross-section. The chalky part and transparent part of the OsAAP3 mutant chalky rice also have obvious variations in the shape, structure, and arrangement of starch grains, but there is no significant difference between the transparent part of the mutant chalky rice and the starch grains of the non-chalky rice. The starch grains in the endosperm center of the OsAAP3 mutant of rice are well developed, but the starch grains in the abdomen and back are loosely arranged, and the starch grains are poorly developed. Therefore, the chalkiness character of OsAAP3 mutant rice increased significantly. The chalkiness character of its mutant mainly occurred in the abdomen, and the rest occurred in the center of the endosperm of rice. Moreover, the arrangement of starch grains in OsAAP3 mutant rice was loose, the grain shape was mostly irregular polyhedrons, and the starch development was poor.

Genetic mechanism of heterosis for rice milling and appearance quality in an elite rice hybrid

Development of hybrid rice with high yield and grain quality is a goal of rice breeding. To investigate the genetic mechanism of heterosis for rice milling and appearance quality in indica/xian rice, QTL mapping was conducted using 1061 recombinant inbred lines (RILs) derived from a cross of the xian rice cultivars Quan9311B (Q9311B) and Wu-shan-si-miao (WSSM), and a backcross F1 (BC1F1) population developed by crossing the RILs with Quan9311A (Q9311A), combined with phenotyping in two environments. The F1 hybrid (Q9311A × WSSM) showed various degrees of heterosis for milling and appearance quality. A total of 142 main-effect QTL (M-QTL) and 407 pairs of epistatic QTL (E-QTL) were identified for five milling and appearance quality traits and grain yield per plant (GYP) in the RIL, BC1F1 and mid-parental heterosis (HMP) populations. Differential detection of QTL in three populations revealed that most additive loci detected in the RILs did not show heterotic effects, but some of them did contribute to BC1F1 trait performance. Unlike heterosis of GYP, single-locus overdominance and epistasis were the main contributors to heterosis for milling and appearance quality. Epistasis contributed more to the heterosis for milling quality than to that for appearance quality. Three (four) QTL regions harboring opposite (consistent) directions of favorable allele effects for GYP and grain quality were identified, indicating the presence of partial genetic overlaps between GYP and grain quality. Three strategies are proposed to develop hybrid rice with high yield and good grain quality: 1) pyramiding favorable alleles with consistent directions of gene effects for GYP and grain quality at the M-QTL on different chromosomes; 2) introgressing favorable alleles for GYP and grain quality into the parents and then pyramiding and fixing these additive effects in hybrids; and 3) pyramiding overdominant and dominant loci and minimizing or eliminating underdominant loci from the parents.

QTL mapping for grain appearance quality traits using doubled haploid population of rice under different environments

QTL mapping for grain appearance quality traits using doubled haploid population of rice under different environments

Detection of QTLs and their environmental interactions for appearance quality traits using two RIL populations in rice

Detection of QTLs and their environmental interactions for appearance quality traits using two RIL populations in rice

Genetic variability, heritability and correlations for milling and grain appearance qualities in some accessions of rice (Oryza sativa L.).

Poor milling and grain appearance is a common feature of locally produced rice (Oryza sativa L.) in West Africa. Development of genotypes with high yield and uniform milled grain size will enhance the market for the locally produced rice. One hundred rice accessions were evaluated to assess genetic variability, heritability and correlations for 11 milling and appearance quality traits and grain yield. The field was laid as a 10 × 10 alpha lattice design with three replications following standard cultivation practices. ANOVA revealed significant differences for the traits studied. The genotypic and environmental variances showed significant differences for all characters studied. Phenotypic coefficient of variation was greater than its corresponding genotypic coefficient of variation for each studied trait. Heritability at broad-sense varied from 14.1% for milling degree to 73.8% for milled grain length-to-width ratio (L/W). Genetic advance as percent of mean ranged from 2.2% for brown rice recovery to 129.6% for percentage of grain with chalkiness (PGWC). In general, genotypic correlations ranged higher than their corresponding phenotypic correlations. Brown rice recovery had significant positive phenotypic and genotypic correlations with milling recovery and head rice recovery. Consequently, brown rice recovery, milling recovery and L/W could be used as selection criteria for the improvement of head rice recovery. Genotypes BETIA and CRI-AMANKWATIA had the desirable PGWC and degree of chalkiness, therefore, they are recommended for the improvement of high yielding varieties with high amount of chalkiness.

Amylose content and grain appearance traits in rice genotypes

Amylose content (AC) and grain appearance traits of rice (Oryza sativa L.) represent a major problem of rice marketing in many rice producing areas in the world. In Uganda, cooking, eating and appearance qualities remain undefined in the rice breeding programme. The objective this study was to determine amylose content of rice genotypes, and its relationship with grain appearance traits; and mode of its inheritance in selected rice genotypes. Forty genotypes were planted in two seasons (2015B and 2016A), in alpha lattice design at National Crop Resource Research Institute in Uganda. Seven parents, involving 3 low and 4 intermediate amylose content genotypes selected in 2015B season,were crossed in a half diallel,and the F1 were advanced to F2 generation, which together with parents were planted in the field. Amylose content (AC), kernel width (KW) and kernel length (K/L) to width ratio were affected by both genetic effects and genotype by season (G x S) interactions; while kernel length was mainly affected by genetic factors. Genotypes were grouped into low, intermediate and high amylose content categories depending on the environment where the genotypes were grown. Three genotypes (Namche 1, P62H17 and 1190) had no significant responsesin amylose content in different growing seasons, suggesting that these genotypes were stable. Amylose content correlated weakly and negatively with physical appearance quality traits of the grain; implying that improvement in amylose content would not affect grain size and shape.There were significant differences (P<0.001) among parents for general combining ability (GCA) and among crosses for specific combining ability (SCA) (P<0.5) for amylose content; indicating that both additive and non-additive gene actions were responsible for the inheritance of AC. However, the variance component of GCA was larger than for the SCA, implying that the inheritance of amylose content was more conditioned by the additive gene effect.Key words: Combining ability, Oryza sativa, Uganda

Dissecting the genome-wide genetic variants of milling and appearance quality traits in rice

Higher head rice yield (HRY), which represents the proportion of intact grains that survive milling, and lower grain chalkiness (opacity) are key quality traits. We investigated the genetic basis of HRY and chalkiness in 320 diverse resequenced accessions of indica rice with integrated single- and multi-locus genome-wide association studies using 2.26 million single-nucleotide polymorphisms. We identified novel haplotypes that underly higher HRY on chromosomes 3, 6, 8, and 11, and that lower grain chalkiness in a fine-mapped region on chromosome 5. Whole-genome sequencing of 92 IRRI breeding lines was performed to identify the genetic variants of HRY and chalkiness. Rare and novel haplotypes were found for lowering chalkiness, but missing alleles hindered progress towards enhancing HRY in breeding material. The novel haplotypes that we identified have potential use in breeding programs aimed at improving these important traits in the rice crop.

Relationships among the chalkiness, kernel size and endosperm cell morphology of rice kernels at different spikelet positions within a panicle

ABSTRACTThe occurrence of chalky kernels in rice is causally related to kernel size and endosperm morphology. This study aimed to investigate the occurrence of chalky kernels by analyzing kernel size, and the number and area of endosperm cells. Spikelets were sampled from upper and middle primary branches and lower secondary branches in a panicle, and divided into four categories: upper, middle, and lower perfect (PF) kernels and lower milky-white (MW) kernels. On the lower secondary branches, there was a higher percentage of chalky kernels, with smaller kernel lengths, widths and thicknesses, than the kernels on the upper and middle primary branches. MW kernels were smaller in size than PF kernels even on the same lower secondary branches. Regardless of grain appearance quality traits, the total areas of endosperm cross sections in lower kernels were significantly smaller than in upper kernels owing to the decreased cell area, and there was a significant negative correlation between the number of cells and average cell area. When the numbers and the areas of cells were analyzed using angular 30° intervals from the line connecting the center point and the dorsal vascular bundle, the MW kernels had significantly less cells than PF kernels near the ventral side at 120–180°. Thus, the decrease in the number of cells near the ventral side was a main causal factor in the decrease in MW kernel widths compared with PF kernel widths, and this suggested that cell division in MW kernels was inhibited at the early grain-filling stage.

QTL Mapping for Rice Appearance Quality Traits Based on a High-density Genetic Map in Different Environments

QTL Mapping for Rice Appearance Quality Traits Based on a High-density Genetic Map in Different Environments

Poultry Meat Quality in Relation to Muscle Growth and Muscle Fiber Characteristics.

Variations in the definition of poultry meat quality exist because the quality traits are not solely based on intrinsic and extrinsic factors but also consumers’ preference. Appearance quality traits (AQT), eating quality traits (EQT), and reliance quality traits (RQT) are the major factors focused by the consumer before buying good quality of poultry meat. AQT and EQT of poultry meat are controlled by physical and biochemical characteristics of muscle fibers which can be categorized into a total number of fibers (TNF), cross-sectional area of fibers (CSAF), and fiber type composition (FTC). In poultry meat, it has been shown that muscle fiber properties play a key role in meat quality because numerous studies have reported the relationships between quality traits and fiber characteristics. Despite intensive research has been carried out to manipulate the muscle fiber to improve poultry meat quality, demand in a rapid growth of poultry muscle has correlated to the deterioration in the meat quality. The present paper reviews the definition of poultry meat quality, meat quality traits, and variations of meat quality. Also, this review presents recent knowledge underlying the relationship between poultry meat quality traits and muscle fiber characteristics.

Identification of quantitative trait loci for rice grain quality and yield-related traits in two closely related Oryza sativa L. subsp. japonica cultivars grown near the northernmost limit for rice paddy cultivation.

Quantitative trait loci (QTLs) associated with eating quality, grain appearance quality and yield-related traits were mapped in recombinant inbred lines (RILs) derived from closely related rice (Oryza sativa L. subsp. japonica) cultivars, Yukihikari (good eating quality) and Joiku462 (superior eating quality and high grain appearance quality). Apparent amylose content (AAC), protein content (PC), brown grain length (BGL), brown grain width (BGWI), brown grain thickness (BGT), brown grain weight per plant (BGW) and nine yield-related traits were evaluated in 133 RILs grown in four different environments in Hokkaido, near the northernmost limit for rice paddy cultivation. Using 178 molecular markers, a total of 72 QTLs were detected, including three for AAC, eight for PC, two for BGL, four for BGWI, seven for BGT, and six for BGW, on chromosomes 1, 2, 3, 4, 6, 7, 8, 9, 11 and 12. Fifteen intervals were found to harbor multiple QTLs affecting these different traits, with most of these QTL clusters located on chromosomes 4, 6, 8, 9 and 12. These QTL findings should facilitate gene isolation and breeding application for improvement of eating quality, grain appearance quality and yield of rice cultivars.

QTL mapping of grain appearance quality traits and grain weight using a recombinant inbred population in rice (Oryza sativa L.)

Grain appearance quality traits, measured as grain length (GL), grain width (GW), length to width ratio (LWR), grain thickness (GT) and the percentage of grain with chalkiness (PGWC), as well as 1 000-grain weight (TGW), are very important factors that contribute to rice grain quality and yield. To detect quantitative trait loci (QTLs) affecting these traits, we developed a set of recombinant inbred lines (RILs) derived from Gang46B (G46B) and K1075, a G46B introgression line with lower PGWC. Based on a linkage map containing 33 simple sequence repeat (SSR) markers, a total of 15 additive QTLs governing six measured traits were identified on 4 chromosomes across two environments. Of these, the five major QTLs which controlled GW, LWR, GT, PGWC, and TGW, each explaining up to 44.30, 55.29, 62.30, 30.94, and 28.78% of the variation, respectively, were found in the same interval of RM18004–RM18068 on chromosome 5. The G46B alleles contributed to the increase in GW, GT and PGWC at all loci, as well as the increase in TGW at its major QTL locus. Significant interactions between additive QTL and the environment were found at most loci, in which the largest, accounting for 15.06% of variation, was observed between qPGWC-5 and the environment. A total of 15 epistasis QTLs were detected for all the traits, and GL, GW and PGWC had significant epistasis QTLs based on environment interactions with minor effects. These results are valuable for future map-based cloning of the QTLs and the collaborative improvement of G46B in grain appearance quality and yield.

Mapping QTL for rice milling and appearance quality traits in <I>indica</I> rice

Quantitative trait loci (QTL) controlling six milling and appearance quality traits were analyzed over 2 years using recombinant inbred lines derived from two indica rice Teqing and IRBB. A total of 30 QTL for these traits were detected, of which eight were for brown rice rate (BRR), two for milled rice recovery (MRR), two for head rice recovery (HRR), seven for grain length (GL), five for grain width (GW), and six for length/width ratio (LWR). The QTL were distributed on all chromosomes except for chromosomes 4 and 12. A QTL cluster with major effects on GL, LWR, BRR, and HRR was located in the RM15139-RM15303 interval on chromosome 3, which includes the GS3 gene for grain size. The phenotypic variances explained by the QTL were 59.51%, 36.68%, 19.51%, and 4.56%, respectively. QTL affecting GW, LWR, BRR, and MRR were clustered in the RM437-RM18038 region of chromosome 5,which covers the GW5 gene for grain width, and contributed 59.51%, 36.68%, 19.51%, and 4.56% to the total variance. QTL with minor effects on BRR and MRR were mapped to the RM190-RM587 interval covering the Wx gene for amylase content on chromosome 6. These results suggest that GS3 and GW5 may play a major roles in the genetic control of BRR and grain shape.

Detection of QTLs with main, epistatic and QTL × environment interaction effects for rice grain appearance quality traits using two populations of backcross inbred lines (BILs)

Quantitative trait loci (QTLs) of rice (Oryza sativa L.) grain appearance traits with additive, epistatic and QTL×environment (QE) interaction effects were studied using a mixed-model-based composite interval mapping (MCIM) method and two populations of back cross inbred lines (BILs) with a common maternal parent. In each of the populations, two or three main effects of QTLs were detected for grain length, width, length to width ratio, length of cooked rice, elongation ratio, elongation index and water absorption traits. The main effects of QTLs explained 12.4–43.9% and 20.4–50.4% of the variation of measured traits in the two populations, respectively. Some identified QTL clusters suggested that co-located QTL or maybe genes with pleiotropic effects could control these traits. When the QTLs detected for cooked versus milled rice were compared, it was found that the main QTLs with large effects for appearance in milled rice were on chromosomes 3 and 5, but those for appearance of cooked rice traits were on chromosome 6 close to the Wx gene. The phenotypic variations which were explained by the effects of the additive×additive×environment interaction (AAE) and additive×additive epistasis (AA) QTLs were less significant than those of the main QTLs. We conclude that although the major genes are frequent determinants of the rice grain appearance traits, the interactions between genes of minor effects may culminate in sizable effects on rice grain appearance traits. The information obtained in this study could be useful for manipulating the QTLs of these traits by molecular marker-assisted selection.

Identification of Quantitative Trait Loci for Rice Quality in a Population of Chromosome Segment Substitution Lines

The demand for high quality rice represents a major issue in rice production. The primary components of rice grain quality include appearance, eating, cooking, physico-chemical, milling and nutritional qualities. Most of these traits are complex and controlled by quantitative trait loci (QTLs), so the genetic characterization of these traits is more difficult than that of traits controlled by a single gene. The detection and genetic identification of QTLs can provide insights into the genetic mechanisms underlying quality traits. Chromosome segment substitution lines (CSSLs) are effective tools used in mapping QTLs. In this study, we constructed 154 CSSLs from backcross progeny (BC(3)F(2)) derived from a cross between 'Koshihikari' (an Oryza sativa L. ssp. japonica variety) as the recurrent parent and 'Nona Bokra' (an O. sativa L. ssp. indica variety) as the donor parent. In this process, we carried out marker-assisted selection by using 102 cleaved amplified polymorphic sequence and simple sequence repeat markers covering most of the rice genome. Finally, this set of CSSLs was used to identify QTLs for rice quality traits. Ten QTLs for rice appearance quality traits were detected and eight QTLs concerned physico-chemical traits. These results supply the foundation for further genetic studies and breeding for the improvement of grain quality.

Effects of Green-Revertible Albino Gene on the Agronomy Traits and Appearance Quality in Rice

Chlorophyll content mutants are important genetic material for photosynthesis and cytoplasmic-nuclear interaction studies, and useful breeding materials for identifying and improving the purity of hybrid seeds. A variant of green-revertible albino (gra) was discovered among the progenies from a crossing of G46B (indica)×Sirio (japonica). A pair of near-isogenic lines (NILs) of Gra and gra were bred by continuously heterozygote self-crossing. The near-isogenic level was evaluated through analysis of polymorphism detected by 120 InDels markers and the results indicated that Gra and gra is a good pair of NILs. Comparative analysis on agronomic and appearance quality traits of NILs indicated that the gra(t)-gene reduced half of the content of chlorophyll at 4-5th leaf stage, and significantly decreased the white root number at transplanting stage, leaf producing speed, tillering ability as well as available spike number and yield per plant. The gra(t)-gene also significantly influenced the length of 2, 3-5, 7, and 9-11th leaves and the width of 3-7 and 9th leaves. However, the gra(t) gene didn't affect the other agronomic traits and the appearance quality of the milled rice investigated in this study.

Analysis of the genetic relationships from different genetic systems between the amylose content and the appearance quality of indica rice across environments

The genetic relationships between amylose content (AC) and appearance quality traits of indica rice (Oryza sativa L.) were investigated using conditional analysis and unconditional analysis in present experiment. The results from the unconditional analysis indicated that AC of rice positively correlated with brown rice (BR, i.e., dehulled but unmilled rice) length (BRL), width (BRW) and thickness (BRT), but was negatively correlated with the ratio of length to width (RLW). The conditional analysis showed that weight of brown rice (WBR) negatively affected the genetic relationships between AC and the appearance quality traits of rice except between AC and BRW, while the genetic relationships between AC and most appearance quality traits were negatively affected by protein content (PC). However, these influences were not apparent due to the impact of WBR or PC on the most covariance components of the different genetic systems between AC and the appearance quality traits. The conditional analysis showed that it was possible to improve AC while significantly reduce BRL and BRT under maintaining WBR. Furthermore, AC could be improved when BRL was reduced under maintaining PC, but BRW and BRT could be significantly increased.

Analysis of the Conditional Correlations from Different Genetic Systems Between the Protein Content and the Appearance Quality Traits of Indica Rice

A factorial mating design in two environments was conducted using 7 cytoplasmic male sterile lines (A) and 5 restorer lines (R) along with their F 1 (A × R) and F 2 populations. The unconditional and conditional analyses of genetic models and the corresponding statistic methods, including endospermic, cytoplasmic, and maternal plant genetic systems, were used to analyze the genetic relationships between protein content (PC) and the appearance quality traits of indica rice ( Oryza sativa L.). The results from unconditional analysis indicated that PC was significantly correlated with the appearance quality traits of rice, except for the brown rice thickness (BRT). Only the genetic covariance between PC and the brown rice width (BRW) was positively correlative, whereas all the other pairwise traits were negatively correlative. The results from conditional analysis revealed that the weight of brown rice (WBR) or the amylose content (AC) could significantly affect the relationships between PC and the appearance quality traits of indica rice. The conditional analysis showed that WBR might negatively affect the relationships between PC and the brown rice length (BRL), BRW, or BRT through the genotype × environmental (GE) interaction effects, but positively affected the relationships between PC and the ratio of brown rice length to width (RLW) or the ratio of brown rice length to thickness (RLT). The amylase content could positively affect the relationships between PC and BRL, RLW, RLT through the cytoplasmic effects and maternal additive effects, but negatively affected the relationships between PC and BRW.

Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments

Rice appearance quality, including traits specifying grain dimension and endosperm chalkiness, represents a major problem in many rice-producing areas of the world. In this study, the genetic basis of six appearance quality traits of milled rice was dissected into quantitative trait loci (QTL) main effects, and the stability of these QTLs was assessed in a population of 66 chromosome segment substitution lines (CSSLs) across eight environments. The CSSLs showed transgressive segregation for many of the traits, and significant correlations were detected among most of the traits. Twenty-two QTLs were identified on eight chromosomes, and numerous QTLs affecting related traits were mapped in the same regions, probably reflecting pleiotropic effects. Nine QTLs, namely qGL-1,qGL-3, qGW-5,qLWR-3, qLWR-5,qPGWC-8, qPGWC-9, qACE-8, and qDEC-8, were consistently detected across the eight environments. The additive main effect and multiplicative interaction (AMMI) analysis showed that genotype (G) x environment (E) interaction was significant for all six traits, with the first three iPCA terms accounting for over 80% of the G x E variance. Both D(I) values and the iPCA1-iPCA2 biplots showed that the CSSLs harboring the nine QTL alleles were more stable than those carrying any of the additional 13 QTL alleles, thereby confirming their environmental stability and pointing to their appropriateness as targets for marker-assisted selection for high-quality rice varieties.