How rice organs are colored: The genetic basis of anthocyanin biosynthesis in rice

Anthocyanins are a major subclass of flavonoids that have diverse biological functions and benefit human health.In rice(Oryza sativa),the various colors shown by organs are due mainly to the accumulation of anthocyanins and are traits associated with domestication.Elucidating the genetic basis of anthocyanin biosynthesis in rice would support the engineering of anthocyanins as well as shedding light on the evolutionary history of O.sativa.We summarize recent progress in rice anthocyanin biosynthesis research,including gene cloning,biosynthetic pathway discovery,and study of the domestication process.We discuss the application of anthocyanin biosynthesis genes in rice breeding.Our object is to broaden knowledge of the genetic basis of anthocyanin biosynthesis in rice and support the breeding of novel rice cultivars.

Analysis on Genetic Diversity and Genetic Basis of the Main Sesame Cultivars Released in China

SRAP （sequence-related amplified polymorphism） was used for the analysis of 67 sesame （Sesamum indicum L.） cultivars widely used in Chinese sesame major production areas from 1950 to 2007. A total of 561 bands were amplified using 21 SRAP random primer pairs, with 265 of them were polymorphic, resulting in a polymorphism ratio of 47.2%. The total bands and polymorphism amplified by each primer pair averaged 26.7 and 12.6, respectively. The average genetic similar coefficient and genetic distance of the 67 cultivars were 0.9104 and 0.0706, respectively, indicating limited genetic diversity and narrow genetic basis. Comparative analysis on genetic similarity and genetic distance of different classified cultivars showed that the difference of average genetic similarity coefficient and genetic distance between the landraces and cultivars bred through crosses reached significant levels （P=0.01）, with the genetic basis of landraces wider than that bred cultivars. The genetic basis of cultivars used in 1990-2007 was more narrow than that of cultivars from 1950 to 1969 and from 1970 to 1989, with the differences of average genetic similarity coefficient and genetic distance reached 0.01 significant level. The genetic basis of Chinese sesame main cultivars is relatively narrow, and the genetic basis of cultivars developed through crosses in recent years is narrower than history cultivars.

Understanding the genetic basis of rice heterosis: Advances and prospects

Heterosis,which describes the superior vigor and yield of F_1 hybrids with respect to their parents,is observed in many rice hybrid crosses.The exploitation of heterosis is a great leap in the history of rice breeding.With advances in genomics and genetics,high-resolution mapping and functional identification of heterosis-associated loci have been performed in rice.Here we summarize advances in understanding the genetic basis of grain yield heterosis in hybrid rice and provide a vision for the genetic study and breeding application of rice heterosis in the future.

Research progress on the divergence and genetic basis of agronomic traits in xian and geng rice

The Asian cultivated rice Oryza sativa can be classified into two major subspecies:japonica/geng and indica/xian.There are large physiological and phenotypic differences between the two subspecies,with each having its advantages and disadvantages.Understanding the differences between xian and geng could provide a foundation for cultivar improvement based on hybridization between subspecies in order to synthesize favorable traits.We review the origin and domestication of xian and geng rice,compare their differences in terms of physiological and phenotypical traits,and describe the molecular mechanism differences between the subspecies.Based on this knowledge,we propose an ideal plant architecture of geng rice varieties for northern regions.

Broadening soybean genetic basis in the northeast of China

The bottle neck of advancement of soybean breeding inthe Northeast of China is the lack of genetic diversity of the parents used in cross breeding.In order to overcome this constrained condition,under the sponsorship of China National Committe of Natural Science Fundation,a network project with the topic'Broadening and Improving of the Genetic Basis of the Northeast Soybeans'was established in 1990,and the Northeast Agricultural University was apointed to take charge of the project.The project included the following four items:Ⅰ.Breeding high yield and improved quality Northeast Soybeans,directed by Hcilongjiang Academy of Agricultural Science.Ⅱ.Development of new soybean gerplasms highly resistant to diseases epidemic in Northeast China directed by Northeast Agricultural university.Ⅲ.Exploitation of the potential of wild and semicultivated soybeans for broadening and improving the genetic basis of Northeast soybeans,directed by Jilin Academy of Agricultural Science.Ⅳ.Improving methods and technique for development of new soybean genetic resources,directed by Nanjing Agricultural University. Each item contained several research subjects conducted by research workers of different institutes of agricultural sciences.During the period 1991-1992,considerable promising new germplasms had been discovered or developed.The new germplasms not only possessed specific improved characters but also behaved with appropriate ecological types adapted to different conditions of Northeast.Among the numerous new germplasms developed,Gong Jio 8757-3 had a protein content of 49.41 %,100 seed weight 16-17 g,and acceptable agronomic characters,which was considered a very valuable new high protein content germplasm.Such developed new germplasms with enforced and improved genetic basis will be used primarily as parents in soybean cross breeding.

Genetic Basis for Mucormycosis Progression in COVID-19 Patients:From Susceptibility to Severity

The dynamics of COVID-19 and mucormycosis reveal a complex interplay of genetic factors that influence the susceptibility,severity,and immune responses.COVID-19,caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),exhibits an increased incidence of mucormycosis,particularly in individuals with comorbidities or corticosteroid therapy.Mucormycosis is a fungal infection that affects the sinuses,orbits,and lungs and demands timely intervention with antifungal medications and surgery because of its life-threatening nature.Research on the genetic underpinnings of this intersection has unveiled key insights into the pathogenicity of Mucorales.Breakthroughs in genetic tools have exposed virulence factors,such as the CotH protein family and high-affinity iron-uptake mechanisms.Genetic susceptibility is a pivotal element in identifying individuals at risk of developing COVID-19,facilitating early detection,and allowing for personalized treatment strategies.DPP9,MIF,and TYK2 are among the genes implicated in COVID-19 severity,emphasizing the intricate relationship between genetic makeup and viral response.The genetic landscape extends to viral entry mechanisms,thereby affecting infection efficiency.Specific polymorphisms in genes such as IFNAR2,OAS3,and TYK2 are associated with COVID-19 severity,indicating shared genetic bases between severe and hospitalized cases.Mucormycosis is genetically predisposed,particularly in immunocompromised individuals.The challenge lies in understanding the genetic factors influencing susceptibility and offering insights into pathogenesis and potential therapeutic avenues.Organ transplantation adds another layer,increasing susceptibility to infections such as COVID-19 and mucormycosis.The impact of immunosuppression on COVID-19 severity remains elusive,necessitating ongoing research on the immunological mechanisms.Despite the challenges posed by emerging SARSCoV-2 variants,the intricate connection between genetic factors and the interplay of COVID-19 and mucormycosis presents an opportunity for personalized treatment,targeted interventions,and refined public health strategies.

Genetic basis for body size variation between an anadromous and two derived lacustrine populations of threespine stickleback Gasterosteus aculeatus in southwest Alaska

Body size is a highly variable trait among geographically separated populations. Size-assortative reproductive isolation has been linked to recent adaptive radiations of threespine stickleback （Gasterosteus aculeatus） into freshwater, but the genetic basis of the commonly found size differ- ence between anadromous and derived lacustrine sticklebacks has not been tested. We studied the genetic basis of size differences between recently diverging stickleback lineages in southwest Alaska using a common environment experiment. We crossed stickleback within one anadromous （Naknek River） and one lake （Pringle Lake） population and between the anadromous and two lake populations （Pringle and JoJo Lakes）, and raised them in a salinity of 4-6 ppt. The F1 anadromous and freshwater forms differed significantly in size, whereas hybrids were intermediate or exhibited dominance toward the anadromous form. Additionally, the size of freshwater Fls differed from their wild counterparts, with within-population Fls from Pringle Lake growing larger than their wild counterparts, while there was no size difference between lab-raised and wild anadromous fish. Sexual dimorphism was always present in anadromous fish, but not in freshwater, and not always in the hybrid crosses. These results, along with parallel changes among anadromous and fresh- water forms in other regions, suggest that this heritable trait is both plastic and may be under di- vergent and/or sexual selection.

Genetic dissection of N use efficiency using maize inbred lines and testcrosses

Although the use of heterosis in maize breeding has increased crop productivity,the genetic causes underlying heterosis for nitrogen(N) use efficiency(NUE) have been insufficiently investigated.In this study,five N-response traits and five low-N-tolerance traits were investigated using two inbred line populations(ILs) consisting of recombinant inbred lines(RIL) and advanced backcross(ABL) populations,derived from crossing Ye478 with Wu312.Both populations were crossed with P178 to construct two testcross populations.IL populations,their testcross populations,and the midparent heterosis(MPH)for NUE were investigated.Kernel weight,kernel number,and kernel number per row were sensitive to N level and ILs showed higher N response than did the testcross populations.Based on a highdensity linkage map,138 quantitative trait loci(QTL) were mapped,each explaining 5.6%–38.8% of genetic variation.There were 52,34 and 52 QTL for IL populations,MPH,and testcross populations,respectively.The finding that 7.6% of QTL were common to the ILs and their testcross populations and that 11.7% were common to the MPH and testcross population indicated that heterosis for NUE traits was regulated by non-additive and non-dominant loci.A QTL on chromosome 5 explained 27% of genetic variation in all of the traits and Gln1-3 was identified as a candidate gene for this QTL.Genome-wide prediction of NUE traits in the testcross populations showed 14%–51% accuracy.Our results may be useful for clarifying the genetic basis of heterosis for NUE traits and the candidate gene may be used for genetic improvement of maize NUE.

Genetic dissection of wheat uppermost-internode diameter and its association with agronomic traits in five recombinant inbred line populations at various field environments

Uppermost-internode diameter(UID)is a key morphological trait associated with spike development and yield potential in wheat.Our understanding of its genetic basis remains largely unknown.Here,quantitative trait loci(QTLs)for UID with high-density genetic maps were identified in five wheat recombinant inbred line(RIL)populations.In total,25 QTLs for UID were detected in five RIL populations,and they were located on chromosomes 1A,1D(3 QTL),2B(2),2D(3),3B,3D,4A,4B(3),4D,5A(5),5B(2),6B,and 7D.Of them,five major and stable QTLs(QUid.sau-2CN-1D.1,QUid.sau-2SY-1D,QUid.sau-QZ-2D,QUid.sau-SC-3D,and QUid.sau-AS-4 B)were identified from each of the five RIL populations in multiple environments.QUid.sau-2CN-1D.1,QUid.sau-2SY-1D and QUid.sau-SC-3D are novel QTLs.Kompetitive Allele Specific PCR(KASP)markers tightly linked to them were further investigated for developing near-isogenic lines(NILs)carrying the major loci.Furthermore,candidate genes at these intervals harboring major and stable QTLs were predicted,and they were associated with plant development and water transportation in most cases.Comparison of physical locations of the identified QTL on the‘Chinese Spring’reference genome showed that several QTLs including two major ones,QUid.sau-2CN-1D.1 and QUid.sau-2 SY-1 D,are likely allelic confirming their validity and effectiveness.The significant relationships detected between UID and other agronomic traits and a proper UID were discussed.Collectively,our results dissected the underlying genetic basis for UID in wheat and laid a foundation for further fine mapping and map-based cloning of these QTLs.

Analysis of Genetic Similarity for Improved Japonica Rice Varieties from Different Provinces and Cities in China

To provide a genetic basis for japonica rice breeding, the genetic similarity and cluster of 139 accessions of improved japonica rice varieties from 12 provinces and cities of China were analyzed using 34 SSR markers. Totally 198 alleles were detected among these improved japonica rice varieties with the average number of alleles per pair of primers was 5.3235. RM320, RM531, RM1, RM286, and RM336 showed more alleles, which were 15, 12, 11, 9, and 9, respectively. RM320, RM336, RM286 and RM531 showed higher genetic diversity indexes; which were 2.3324, 2.0292, 1.8996, and 1.7820, respectively. The range of genetic similar index among improved japonica rice varieties from different provinces was from 0.321 to 0.914, with the average of 0.686. There was a high genetic similarity among improved japonica rice varieties from Heilongjiang, Jilin, Liaoning, Ningxia, and Yunnan, which were located in similar latitude or similar ecological environment, while there was a low genetic similarity between improved japonica rice varieties from Guizhou and Jiangsu, and other provinces which were located in more different latitudes and ecological environments. The markers of RM320, RM531, RM1, RM286, and RM336 fit to be used in analysis of genetic diversity for improved japonica rice variety. The genetic similarity among improved japonica rice varieties from different provinces was closely associated with genetic basis of parents, and was also correlated with latitude and ecological environment where the varieties were bred.

Prospects of utilization of inter-subspecific heterosis between indica and japonica rice

The Asian cultivated rice(Oryza sativa L.) grown worldwide is divided into two subspecies, indica and japonica. It is well known that the heterosis of inter-subspecies is usually stronger than that of intra-subspecies. Since the 1970 s, indica hybrid rice, an intra-subspecific hybrid rice, has being widely used in China and even in the world. However, the inter-subspecific hybrid rice between indica and japonica is still unavailable. The major obstacle is the hybrid sterility of the inter-subspecies. In recent decades, the genetic and molecular basis of indica-japonica hybrid sterility was understood more and more clearly. Some breeding approaches for overcoming inter-subspecific hybrid sterility were proposed and used to develop the indicajaponica hybrid rice. The updated understanding will offer new approaches for development of breeding lines for overcoming indica-japonica hybrid sterility, which facilitates developing of inter-subspecific hybrid rice.

Mapping QTL for flowering time-related traits under three plant densities in maize

Flowering time is an indicator of adaptation in maize and a key trait for selection in breeding.The genetic basis of flowering time in maize,especially in response to plant density,remains unclear.The objective of this study was to identify maize quantitative trait loci(QTL)associated with flowering time-related traits that are stably expressed under several plant densities and show additive effects that vary with plant density.Three hundred recombinant inbred lines(RIL)derived from a cross between Ye 478 and Qi 319,together with their parents,were planted at three plant densities(90,000,120,000,and 150,000 plants ha^(-1))in four environments.The five traits investigated were days to tasseling(DTT),days to silking(DTS),days to pollen shed(DTP),interval between anthesis and silking(ASI),and interval between tasseling and anthesis(TAI).A high-resolution bin map was used for QTL mapping.In the RIL population,the DTT,DTS,and DTP values increased with plant density,whereas the ASI and TAI values showed negligible response to plant density.A total of 72 QTL were identified for flowering time-related traits,including 15 stably expressed across environments.Maize flowering time under different densities seems to be regulated by complex pathways rather than by several major genes or an independent pathway.The effects of some stable QTL,especially qDTT8-1 and qDTT10-4,varied with plant density.Fine mapping and cloning of these QTL will shed light on the mechanism of flowering time and assist in breeding earlymaturing maize inbred lines and hybrids.

The genetic and molecular basis for improving heat stress tolerance in wheat

Wheat production requires at least-2.4%increase per year rate by 2050 globally to meet food demands.However,heat stress results in serious yield loss of wheat worldwide.Correspondingly,wheat has evolved genetic basis and molecular mechanisms to protect themselves from heat-induced damage.Thus,it is very urgent to understand the underlying genetic basis and molecular mechanisms responsive to elevated temperatures to provide important strategies for heat-tolerant varieties breeding.In this review,we focused on the impact of heat stress on morphology variation at adult stage in wheat breeding programs.We also summarize the recent studies of genetic and molecular factors regulating heat tolerance,including identification of heat stress tolerance related QTLs/genes,and the regulation pathway in response to heat stress.In addition,we discuss the potential ways to improve heat tolerance by developing new technologies such as genome editing.This review of wheat responses to heat stress may shed light on the understanding heat-responsive mechanisms,although the regu-latory network of heat tolerance is still ambiguous in wheat.

Genetic architecture and molecular regulation of sorghum domestication

Over time,wild crops have been domesticated by humans,and the knowledge gained from parallel selection and convergent domestication-related studies in cereals has contributed to current techniques used in molecular plant breeding.Sorghum(Sorghum bicolor(L.)Moench)is the world’s fifth-most popular cereal crop and was one of the first crops cultivated by ancient farmers.In recent years,genetic and genomic studies have provided a better understanding of sorghum domestication and improvements.Here,we discuss the origin,diversification,and domestication processes of sorghum based on archeological discoveries and genomic analyses.This review also comprehensively summarized the genetic basis of key genes related to sorghum domestication and outlined their molecular mechanisms.It highlights that the absence of a domestication bottleneck in sorghum is the result of both evolution and human selection.Additionally,understanding beneficial alleles and their molecular interactions will allow us to quickly design new varieties by further de novo domestication.

Advances in the Research of Strategies and Methods for Analyzing Complex Traits

Complex traits are the features whose properties are determined by both genetic and environmental factors. Generally, complex traits include the classical quantitative traits with continuous distribution, the binary or categorical traits with discrete distribution controlled by polygene and other traits that cannot be measured exactly, such as behavior and psychology. Most human complex diseases and most economically important traits in plants and animals belong to the category. Understanding the molecular basis of complex traits plays a vital role in the genetic improvement of plant and animal breeding. In this article, the conception and research background of complex traits were summarized, and the strategies, methods and the great progress that had been made in dissecting genetic basis of complex traits were reviewed. The challenges and possible developments in future researches were also discussed.

Genetic architecture and key genes controlling the diversity of oil composition in rice grains

Rice grain oil is a valuable nutrient source.However,the genetic basis of oil biosynthesis in rice grains remains unclear.In this study,we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions.High variation for 11 oil-related traits was observed,and the oil composition of rice grains showed differentiation among the subpopulations.We identified 46 loci that are significantly associated with grain oil concentration or composition,16 of which were detected in three recombinant inbred line populations.Twenty-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci,four of which(PAL6,LIN6,MYR2,and ARA6)were found to contribute to natural variation in oil composition and to show differentiation among the subpopulations.Interestingly,population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica rice.Based on these results,we propose a possible oil biosynthetic pathway in rice grains.Collectively,our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.