Mapping and Validation of QTLs for the Amino Acid and Total Protein Content in Brown Rice

QTL detection for rice grain storage protein content and genetic effect verifications

Rice grain quality is a multifarious attribute mainly governed by multiple nutritional factors. Grain protein is the central component of rice grain nutrition dominantly affecting eating-cooking qualities. Grain protein content is quantitatively influenced by its protein fractions. Genetic quantification of five protein fractions-albumins, globulins, prolamins, glutelin, and grain protein content-were evaluated by exploiting two BC3F2 mapping populations, derived from Kongyu131/TKM9 (population-I) and Kongyu131/Bg94-1 (population-II), which were grown in a single environment. Correlation studies among protein fractions and grain protein content were thoroughly investigated. A genetic linkage map was developed by using 146 single sequence repeat (SSR) markers in population-I and 167 markers in population-II. In total, 40 QTLs were delineated for five traits in both populations. Approximately 22 QTLs were dissected in population-I, derived from Kongyu131/TKM9, seven QTLs for albumin content, four QTLs for globulin content, three QTLs for prolamin content, four QTLs for glutelin content, and four QTLs for grain protein content. In total, 18 QTLs were detected in population-II, derived from Kongyu131/Bg94-1, five QTLs for albumin content, three QTLs for globulin content, four QTLs for prolamin content, two QTLs for glutelin content, and four QTLs for grain protein content. Three QTLs, qAlb7.1, Alb7.2, and qGPC7.2, derived from population-II (Kongyu131/Bg94-1) for albumin and grain protein content were successfully validated in the near isogenic line (NIL) populations. The localized chromosomal locus of the validated QTLs could be helpful for fine mapping via map-based cloning to discover underlying candidate genes. The functional insights of the underlying candidate gene would furnish novel perceptivity for the foundation of rice grain protein content and trigger the development of nutritionally important rice cultivars by combining marker-assisted selection (MAS) breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01436-7.

Genetic control of grain amino acid composition in a UK soft wheat mapping population

Wheat (Triticum aestivum L.) is a major source of nutrients for populations across the globe, but the amino acid composition of wheat grain does not provide optimal nutrition. The nutritional value of wheat grain is limited by low concentrations of lysine (the most limiting essential amino acid) and high concentrations of free asparagine (precursor to the processing contaminant acrylamide). There are currently few available solutions for asparagine reduction and lysine biofortification through breeding. In this study, we investigated the genetic architecture controlling grain free amino acid composition and its relationship to other traits in a Robigus × Claire doubled haploid population. Multivariate analysis of amino acids and other traits showed that the two groups are largely independent of one another, with the largest effect on amino acids being from the environment. Linkage analysis of the population allowed identification of quantitative trait loci (QTL) controlling free amino acids and other traits, and this was compared against genomic prediction methods. Following identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. These findings can be used to select appropriate strategies for lysine biofortification and free asparagine reduction in wheat breeding programs.

Association mapping for protein, total soluble sugars, starch, amylose and chlorophyll content in rice

BACKGROUND

Protein, starch, amylose and total soluble sugars are basic metabolites of seed that influence the eating, cooking and nutritional qualities of rice. Chlorophyll is responsible for the absorption and utilization of the light energy influencing photosynthetic efficiency in rice plant. Mapping of these traits are very important for detection of more number of robust markers for improvement of these traits through molecular breeding approaches.

RESULTS

A representative panel population was developed by including 120 germplasm lines from the initial shortlisted 274 lines for mapping of the six biochemical traits using 136 microsatellite markers through association mapping. A wide genetic variation was detected for the traits, total protein, starch, amylose, total soluble sugars, chlorophyll a, and chlorophyll b content in the population. Specific allele frequency, gene diversity, informative markers and other diversity parameters obtained from the population indicated the effectiveness of utilization of the population and markers for mapping of these traits. The fixation indices values estimated from the population indicated the existence of linkage disequilibrium for the six traits. The population genetic structure at K = 3 showed correspondence with majority of the members in each group for the six traits. The reported QTL, qProt1, qPC6.2, and qPC8.2 for protein content; qTSS8.1 for total soluble sugar; qAC1.2 for amylose content; qCH2 and qSLCHH for chlorophyll a (Chl. a) while qChl5D for chlorophyll b (Chl. b) were validated in this population. The QTL controlling total protein content qPC1.2; qTSS7.1, qTSS8.2 and qTSS12.1 for total soluble sugars; qSC2.1, qSC2.2, qSC6.1 and qSC11.1 for starch content; qAC11.1, qAC11.2 and qAC11.3 for amylose content; qChla8.1 for Chl. a content and qChlb7.1 and qChlb8.1 for Chl. b identified by both Generalized Linear Model and Mixed Linear Model were detected as novel QTL. The chromosomal regions on chromosome 8 at 234 cM for grain protein content and total soluble sugars and at 363 cM for Chl. a and Chl. b along with the position at 48 cM on chromosome 11 for starch and amylose content are genetic hot spots for these traits.

CONCLUSION

The validated, co-localized and the novel QTL detected in this study will be useful for improvement of protein, starch, amylose, total soluble sugars and chlorophyll content in rice.

Contrasting Water Withholding Responses of Young Maize Plants Reveal Link Between Lipid Peroxidation and Osmotic Regulation Corroborated by Genetic Analysis

Linking biochemistry and genetics of tolerance to osmotic stress is of interest for understanding plant adaptations to unfavorable conditions. The aims of this study were to investigate the variability in responses of panel of elite maize inbred lines to water withholding for stress-related traits through association study and to identify pathways linked to detected associations for better understanding of maize stress responses. Densely genotyped public and expired Plant Variety Protection Certificate (ex-PVP) inbred lines were planted in controlled conditions (16-h/8-h day/night, 25°C, 50% RH) in control (CO) and exposed to 10-day water withholding (WW). Traits analyzed were guaiacol peroxidase activity (GPOD), total protein content (PROT), lipid peroxidation (TBARS), hydrogen peroxide accumulation (H₂O₂), proline accumulation (proline), and current water content (CWC). Proline accumulation was found to be influenced by H₂O₂ and TBARS signaling pathways acting as an accumulation-switching mechanism. Most of the associations detected were for proline (29.4%) and TBARS (44.1%). Gene ontology (GO) enrichment analysis showed significant enrichment in regulation of integral membrane parts and peroxisomes along with regulation of transcription and polysaccharide catabolism. Dynamic studies involving inbreds with extreme phenotypes are needed to elucidate the role of this signaling mechanism in regulation of response to water deficit.

Consensus genetic map and QTLs for morphological and agronomical traits in mungbean using DArT markers

Mungbean is an important but understudied food legume compared with other major grain crops. Genetic studies through development of high-through put markers, linkage map construction and QTL analysis can accelerate and improve the efficiency of mining for genes for breeding in this crop. This study used four mungbean F₅ recombinant inbred lines (RILs) from crosses of two wild types (ACC 1, ACC 87) and two cultivars (Berken, Kiloga) and DArT markers to construct individual and consensus linkage maps and to identify QTLs associated with 54 traits in mungbean. The number of polymorphic DArT markers identified among the four RIL populations varied from 1062 to 2013. The individual maps covered the lengths of 629.7-883.5 cM, comprising 672-981 DArT markers and 15-19 linkage groups (LG) with average distance between markers of 0.9-1.2 cM. The consensus map had the total length of 795.3 cM, comprising 1539 DArT markers and resolved 11 LGs with an average inter-marker distance of 0.65 cM. Sixty-two QTLs were identified for 39 traits across 10 LGs of the consensus map. Major QTLs were identified for two special traits, late flowering inherited from ACC 1 (6 QTLs, PVE of 11.2-29.9%) and perenniality inherited from ACC 87 (3 QTLs, PVE of 17.4-22.6%) in separate population analysis. Number of congruent QTLs across four mungbean populations and the consensus map was 18 for 13 traits. These results illustrated the high efficiency of DArT marker application in mungbean genetic dissection and suggested the future potential employment of identified QTLs for mungbean improvement.

Enhancing health benefits of milled rice: current status and future perspectives

Milled rice is an essential part of the regular diet for approximately half of the world's population. Its remarkable commercial value and consumer acceptance are mostly due to its promising cooking qualities, appealing sensory properties, and longer shelf life. However, the significant loss of the nutrient-rich bran layer during milling makes it less nutritious than the whole grain. Thus, enhancing the nutritive value of milled rice is vital in improving the health and wellbeing of rice consumers, particularly for those residing in the low-economic zones where rice is the primary source of calories and nutrition. This article provides a critical review on multiple frontiers of recent interventions, such as (1) infusing the genetic diversity to enrich amylose and resistant starch to reduce glycaemic index, (2) enhancing the minerals and vitamins through complementary fortification and biofortification as short and long-term interventions, and (3) developing transgenic solutions to improve the nutrient levels of milled rice. Additionally, the review highlights the benefits of functional ingredients of milled rice to human health and the potential of enhancing them in rice to address the triple burden of malnutrition. The potential merit of milled rice concerning food safety is also reviewed in this article.

Major QTLs, qARO1 and qARO9, Additively Regulate Adaxial Leaf Rolling in Rice

Moderate leaf rolling is considered optimal for the ideal plant type in rice (Oryza sativa L.), as it improves photosynthetic efficiency and, consequently, grain yield. Determining the genetic basis of leaf rolling via the identification of quantitative trait loci (QTLs) could facilitate the development of high-yielding varieties. In this study, we identified three stable rice QTLs, qARO1, qARO5, and qARO9, which control adaxial leaf rolling in a recombinant inbred line (RIL) population derived from a cross between Tong 88-7 (T887) and Milyang 23 (M23), using high-density SNP markers. These QTLs controlled the rolling phenotype of both the flag leaf (FL) and secondary leaf (SL), and different allelic combinations of these QTLs led to a wide variation in the degree of leaf rolling. Additive gene actions of qARO1 and qARO9 on leaf rolling were observed in a backcross population. In addition, qARO1 (markers: 01id4854718 and 01asp4916781) and qARO9 (markers: 09id19650402 and 09id19740436) were successfully fine-mapped to approximately 60- and 90-kb intervals on chromosomes 1 and 9, respectively. Histological analysis of near-isogenic lines (NILs) revealed that qARO1 influences leaf thickness across the small vein, and qARO9 affects leaf thickness in the entire leaf and bulliform cell area, thus leading to adaxial leaf rolling. The results of this study advance our understanding of the genetic and molecular bases of adaxial leaf rolling, and this information can be used for the development of rice varieties with the ideal plant type.

Enhancing the Nutritional Quality of Major Food Crops Through Conventional and Genomics-Assisted Breeding

Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.