Application of near-infrared spectroscopy for fast germplasm analysis and classification in multi-environment using intact-seed peanut(Arachis hypogaea L.)

Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional breeding.In this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess germplasm variability from whole seed of 699 samples,field-collected and assembled in four genetic and environmentbased sets:one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population,evaluated in three environments in a large spatial scale of two countries,Mbalmayo and Bafia in Cameroon and Nioro in Senegal,under rainfed conditions.NIR elemental spectra were gathered on six subsets of seeds of each sample,after three rotation scans,with a spectral resolution of 16 cm-1over the spectral range of867 nm to 2530 nm.Spectra were then processed by principal component analysis(PCA)coupled with Partial least squares-discriminant analysis(PLS-DA).As results,a huge variability was found between varieties and genotypes for all NIR wavelength within and between environments.The magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 nm,usually related to oil content and fatty acid composition.PCA yielded the most chemical attributes in three significant PCs(i.e.,eigenvalues>10),which together captured 93%of the total variation,revealing genetic and environment structure of varieties and genotypes into four clusters,corresponding to the four samples sets.The pattern of genetic variability of the interspecific population covers,remarkably half of spectrum of the core-collection,turning out to be the largest.Interestingly,a PLS-DA model was developed and a strong accuracy of 99.6%was achieved for the four sets,aiming to classify each seed sample according to environment origin.The confusion matrix achieved for the two sets of Bafia and Nioro showed 100%of instances classified correctly with 100%at both sensitivity and specificity,confirming that their seed quality was different from each other and all other samples.Overall,NIRS chemometrics is useful to assess and distinguish seeds from different environments and highlights the value of the interspecific population and core-collection,as a source of nutritional diversity,to support the breeding efforts.

Selection criteria of MPOB-Angola germplasm collection for yield improvement of the oil palm

Oil palm germplasm collected from Angola,Africa in 1991 were subjected to genetic variability potential studies.The collection was planted in the form of open-pollinated families as trials at the Malaysian Palm Oil Board(MPOB)Kluang Research Station,Johor,Malaysia,in 1994.Dura palms from 52 families and tenera palms from 44 families of MPOB-Angola were evaluated for their bunch yield and bunch quality components.The objectives of this study were to determine the genetic variability among the families and performance of MPOB-Angola germplasm for yield improvement.The analysis of variance(ANOVA)revealed highly significant differences between the dura and tenera families for most of the traits,suggesting the presence of high genetic variability,which is essential for breeding programmes.Among the duras,family AGO 02.02 displayed the best yield performance,with a high fresh fruit bunch,oil yield and total economic product at 240.40,29.46 and 37.93 kg palm^(-1)year^(-1),respectively.As for the teneras,family AGO 03.04 recorded the highest FFB yield and oil yield at 249.25 and 45.22 kg palm^(-1)year^(-1),respectively.Besides that,several families with big fruit sizes or producing a mean fruit weight of 14-17 g were also identified.Both dura and tenera from AGO 01.01 recorded the highest oil to bunch(O/B)of 17.76%and 28.65%,respectively.These findings will facilitate the selection of palms from the MPOB-Angola germplasm for future breeding programmes.

Correction:Identification of SSR markers linked to the abscission of cotton boll traits and mining germplasm in Cotton

Correction:J Cotton Res 7,20(2024)https://doi.org/10.1186/s42397-024-00180-3 Following publication of the original article(Shui et al.2024),the author found 5 errors in the published article.1.One of the author’s name has been corrected from Gou Chunping to Guo Chunping.2.The reference(Zhao SQ.2016)in Table 2 has been updated to:Zhao SQ.Analysis on the major gene and multigene mixed inheritance and QTL mapping for early maturity traits in upland cotton.Chin Acad Agric Sci.2016.https://doi.org/10.3969/j.issn.201600501.(in Chinese with English abstract).3.In’Results’part,’Phenotype analysis of 238 cotton boll abscission among cotton accessions’paragraph,the phenotype analysis of AR1 ranging from 19.27%–63.79%,which was wrongly written as 19.27%-63.97%.4.The‘2018KRL’is modified to‘2018KEL’in Table 1.

Extent and Structure of Phenotypic Variability in Solenostemon rotundifolius Germplasm from Ghana and Burkina Faso

Solenostemon rotundifolius is a species belonging to the Lamiaceae family. It is currently one of the minor plants of high socio-economic interest. One of the limitations to promoting this species in Burkina Faso is the lack of varieties that meet consumers’ demands. Implementing a breeding program is an important step toward achieving this goal. Such a program is based on the variability of agronomical traits of interest within evaluated germplasm. This study aimed to assess the level of two germplasms variability of S. rotundifolius from Ghana and Burkina Faso for traits related to vegetative development, cycle, and yield. Agromorphological characterization of 174 accessions, including 116 from Ghana and 58 from Burkina Faso was carried out in Randomised Complete Block Design with three replications. The characterization was made on the basis of fifteen (15) quantitative traits related to the canopy and leaf size, the cycle, and the yield. Analysis of variance revealed significant differences between accessions within each germplasm for all the evaluated traits. The analysis of the structuration of this agromorphological variability allowed organizing the accessions into different groups. These results could lead to the identification of accessions within each germplasm for breeding purposes or future research on genotype-environment interactions.

Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits

Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity,which limits gene mining for important agronomic traits.Here,314 sweetpotato germplasm resources were deeply resequenced,and 4599509 SNPs and 846654 InDels were generated,among which 196124 SNPs were nonsynonymous and 9690 InDels were frameshifted.Based on the Indels,genome-wide marker primers were designed,and 3219 of 40366 primer pairs were selected to construct the core InDel marker set.The molecular ID of 104 sweetpotato samples verified the availability of these primers.The sweetpotato population structures were then assessed through multiple approaches using SNPs,and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources.As many as 20 important agronomic traits were evaluated,and a genome-wide association study was conducted on these traits.A total of 19 high-confidence loci were detected in both models.These loci included several candidate genes,such as IbMYB1,IbZEP1,and IbYABBY1,which might be involved in anthocyanin metabolism,carotenoid metabolism,and leaf morphogenesis,respectively.Among them,IbZEP1 and IbYABBY1 were first reported in sweetpotato.The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with f lesh color(orange or not orange)in sweetpotato.The expression levels of IbYABBY1 were also correlated with leaf shape.These results will assist in genetic and breeding studies in sweetpotato.

Genome-wide association mapping in a sweet cherry germplasm collection(Prunus avium L.)reveals candidate genes for fruit quality traits

In sweet cherry(Prunus avium L.),large variability exists for various traits related to fruit quality.There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands.With this objective,a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2-6 years,and characterized using a genotyping-by-sequencing approach.The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes.We identified numerous SNP-trait associations for global fruit size(weight,width,and thickness),fruit cracking,fruit firmness,and stone size,and we pinpointed several candidate genes involved in phytohormone,calcium,and cell wall metabolisms.Finally,we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker-trait associations.This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality,and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.

Generating colorful carrot germplasm through metabolic engineering of betalains pigments

Betalains are tyrosine-derived plant pigments exclusively found in the Caryophyllales order and some higher fungi and generally classified into two groups:red-violet betacyanins and yellow-orange betaxanthins.Betalains attract great scientific and economic interest because of their relatively simple biosynthesis pathway,attractive colors and health-promoting properties.Co-expressing two core genes BvCYP76AD1 and BvDODA1 with or without a glycosyltransferase gene MjcDOPA5GT allowed the engineering of carrot(an important taproot vegetable)to produce a palette of unique colors.The highest total betalains content,943.2μg·g^(−1) DW,was obtained in carrot taproot transformed with p35S:RUBY which produces all of the necessary enzymes for betalains synthesis.Root-specific production of betalains slightly relieved tyrosine consumption revealing the possible bottleneck in betalains production.Furthermore,a unique volcano-like phenotype in carrot taproot cross-section was created by vascular cambium-specific production of betalains.The betalains-fortified carrot in this study is thus anticipated to be used as functional vegetable and colorful carrot germplasm in breeding to promote health.

Assessing genetic variation in Gossypium barbadense L.germplasm based on fibre characters

Background Gossypium barbadense L.has specific fibre in terms of its length,strength,and fineness,and known as extra-long staple(ELS) cotton,Sea–Island cotton,or Egyptian cotton.Narrow genetic base with less genetic variability is observed in G.barbadense germplasm.Hence,this study was aimed to evaluate the genetic variability present in 108 germplasm accessions of G.barbadense and to identify the superior genotypes based on the fibre traits.Results We evaluated 108 accessions for five fibre quality traits along with three checks in augmented block design.All fibre traits showed significant differences among genotypes,indicating that there is genetic potential for improvement.Fibre strength and micronaire(MIC) showed high phenotypic and genotypic coefficients of variation.High heritability combined with high genetic advance as percentage of mean(GAM) was recorded for fibre length,strength,and micronaire.Fibre strength and fibre length were significantly correlated with each other,while both showed negative correlation with micronaire.Principal component analysis and Biplot analysis showed that uniformity index discriminated all the genotypes in higher level,while fibre length and strength were medium in discrimination power.Biplot revealed genotypes DB 16,EC959191,GSB 39,ARBB 20,5746U,EA 203,and EA 201 were genetically diverse.Hierarchal cluster analysis based on unweighted paired group method using arithmetic average(UPGMA) grouped the genotypes into four clusters,with each cluster consisting of 4,18,48,and 38 genotypes,respectively.Conclusion Among the genotypes,34 for fibre length(> 35 mm),18 for fibre strength(> 40.4 g·tex^(-1)) and 66 for micronaire(3.7-4.2,A grade) were identified as potential accessions based on their superiority.The superior fibre genotypes identified in this study are potential lines for the ELS cotton breeding program.

Synthetical Evaluation on the Qualitative and Quantitative Resistance of Rice Germplasms to Magnaporthe oryzae

[Objectives]This study was conducted to screen out rice resources resistant to rice blast(Magnaporthe oryzae).[Methods]The qualitative and quantitative resistance of 1659 rice resources from 45 countries and regions to rice blast were evaluated by disease nursery in upland condition and the test of the spectrum to rice blast isolates.[Results]There were 292 entries which accounted for 17.6%showed high blast resistance(0 and 1 disease scale),68 entries(counted for 4.1%)showed resistance to blast(3 disease scale);and the number of the entries showed intermediate resistance,intermediate susceptible and susceptible were 208(with the corresponding percentage of 12.5%),471(28.4%),620(37.4%)respectively.Among the tested entries,27 entries including BG1222,BL122,BTX,IR37704-131-2-3-2,and LEBONNET had showed broad-spectrum blast resistance with the resistance frequency of higher than 90%,Quantitative resistance evaluation was conducted on some key resources,and 14 entries,of which are BR27,DRAGO,IR100,QINLIUAI、SERIBU GANTANG,YUEXIANGZHAN and so on,showed good quantitative resistances,and 8 entries had higher quantitative resistances than IR36.[Conclusions]This study provides important blast resistance resources for the local rice breeding program and has a significant value for the discovery of new blast resistance genes and its application in the blast resistance breeding.

Protection and Utilization of Chinese Giant Salamander Germplasm Resources

Chinese giant salamander(Andrias davidianus)is salamander germplasm resource that only distributed in China.It is the material basis of the evolution principle research,genetic research and artificial breeding.Since the 1990s,overharvesting,water pollution and habitat changes have seriously destroyed the germplasm resources of A.davidianus,their population density has decreased since then.Strengthening the protection and rational utilization of A.davidianus germplasm resources are key factors in impacting the healthy,stable and sustainable development of A.davidianus industry.Under the above background,we discussed the current problems with the protection for A.davidianus germplasm resources,put forward suggestions for the conservation of A.davidianus germplasm resources.It is expected to provide a reference to effective protection for A.davidianus germplasm resources,and provide a scientific foundation for further studies,so as to promote the high-quality development of related industry.

Evaluation and Exploration of Citrus Germplasm Resources in the Origin of Shatangju(Citrus flamea Hort.ex Tseng Shiyueju)

[Objectives]To protect the local rare citrus germplasm resources and further develop and cultivate new citrus varieties.[Methods]The germplasm resources of Shatangju(Citrus flamea Hort.Ex Tseng Shiyueju)in Sihui City of Guangdong Province and other 8 citrus varieties from the same origin were evaluated.The appearance characteristics of tree shape,the length and thickness of shoot at each shoot stage,the appearance characteristics of leaves and the fruit quality of each variety were investigated.[Results]Through the comparison of various citrus varieties grafted with sour mandarin,the results showed that the overall advantages of the length and thickness of the shoots of Shatang tangerine in summer and autumn were more prominent,which was conducive to fruit setting.The sprouting time of the three shoots of each variety was different,and there were sporadic sprouting phenomena in different seasons,so the growth was different,and the length and thickness of the shoots were different in different seasons.There were significant differences in shoot length and diameter among different varieties in the same season.The coefficient of variation of Shatangju's leaves was low,and the traits were stable;leaf shape,leaf base shape,leaf margin and other indicators among the three shoots of the same variety and the differences among the same shoots of different varieties were compared.All varieties had strong flavor,separately sweet and sour,sweet and sweet taste.Shatangju has many segments,orange pericarp,rough texture,easy peeling,and high oblate fruit shape.The orange pericarp was favored by the participants,while the rough and thick peel was not favored by the participants.[Conclusions]Based on the improvement of local varieties,it is recommended to improve the smoothness of pericarp,reducing the thickness of pericarp and improving the flavor of fruit will be conducive to increasing sales.In the cultivation process of various quality resources,especially in the period of fruit growth and development,the plan of nutrition and fertilization should be formulated according to the rules of fruit growth and development,the rules of yield formation and the rules of quality composition,so as to establish the integrated nutrient management system of various varieties.

Genomics-based plant germplasm research(GPGR)

Plant germplasm underpins much of crop genetic improvement.Millions of germplasm accessions have been collected and conserved ex situ and/or in situ,and the major challenge is now how to exploit and utilize this abundant resource.Genomics-based plant germplasm research(GPGR) or "Genoplasmics" is a novel cross-disciplinary research field that seeks to apply the principles and techniques of genomics to germplasm research.We describe in this paper the concept,strategy,and approach behind GPGR,and summarize current progress in the areas of the definition and construction of core collections,enhancement of germplasm with core collections,and gene discovery from core collections.GPGR is opening a new era in germplasm research.The contribution,progress and achievements of GPGR in the future are predicted.

Advances in Germplasm Resources of Chinese Milk Vetch in China

Chinese milk vetch （Astragalus sinicus L. ） is a conunonly used green manure crop in paddy fields in southern China and it has the effect of fostering fertility and soil. This paper firstly sununarized advances in research of new high quality and yield varieties of germplasm resources of Chinese milk vetch. Then, on the basis of current situation, it came up with recommendations for collection, storage and promotion, as well as application in the current ecological agriculture, including establishing germplasm resource bank and improving germplasm resource evaluation system.

Construction of Transgenic Crop Germplasm Effective Function and Characteristic Analysis

Germplasm effect reflects the quantitative relation between production ability of germplasm elements and yield （quality） of a certain crop, which can be shown by mathematic function, namely, germplasm effect function. Germplasm effect of a crop variety is an aggregation of many effective factors, and is restrained by different effective factors; constant increase of any one effect of germplasm elements would lead to law of effect decline, therefore, possible modes of transgenic crops effect function were deduced according to the law of effect decline. The possible modes of single transgenic germplasm effect function and multi-transgenic germplasm effect regression equation were discussed, and the characteristics of germplasm effect regression equation were analyzed in this paper.

Genetic Variation in Rhizome Lotus(Nelumbo nucifera Gaertn.ssp.nucifera) Germplasms from China Assessed by RAPD Markers

To estimate genetic variation in rhizome lotus （Nelumbo nucifera Gaertn. ssp. nucifera） germplasms in China, a total of 94 rhizome lotus germplasms collected from 18 provinces in China were assessed. The RAPD （randomly amplified polymorphic DNA） marker was employed. The selected 17 random primers detected 139 polymorphic alleles out of a total 207 （67.15%）. Nei＇s gene diversity statistics and region differentiation parameters indicated that all germplasms had a relatively high level of genetic diversity with ne = 1.3202, h = 0.1937, I= 0.2982 and the gene flow among all regions was Nrn = 5.5742. The UPGMA dendrogram clustered all 94 germplasms into two clusters： One contained eight commercial cultivars and major landraces, and the other included the wild and some special landraces from five regions, and the PCA analysis exhibited the similar result. Those germplasms from southwestern and eastern China had higher genetic diversity than those from the southern, northern and central China. Predominant proportion of genetic variation （95.61%） was found significant within rather than among （4.39%） regions, as revealed by AMOVA analysis. The data analysis also revealed that the genetic diversity of rhizome lotus germplasms among different regions is positively related to their geographic distances, though it is ambiguous to find the trend from the UPGMA dendrogram and the PCA analysis. A relatively high genetic diversity and gene flow resided in the root lotus germplasms; about 96% of the variation was found within region; accessions from southwest and eastern China have higher genetic diversity than those from the southern, northern and central China.

Genetic diversity and population structure analysis of Capsicum germplasm accessions

Genetic diversity plays an essential role in plant breeding and utilization.Pepper is an important vegetable and spice crop worldwide.The genetic diversity of 1 904 accessions of pepper conserved at the National Mid-term Genebank for Vegetables,Beijing,China was analyzed based on 29 simple sequence repeat(SSR)markers,which were evenly distributed over 12 pepper chromosomes.The pepper accessions were divided into two groups in a genetic structure analysis,and the two groups showed obvious differences in fruit type and geographical distribution.We finally selected 248 accessions capturing 75.6%of the SSR alleles as the core collection for further research.Insights into the genetic structure of pepper provide the basis for population-level gene mining and genetic improvement.

Introduction and Utilization of INGER Rice Germplasm in China

The International Network for Genetic Evaluation of Rice (INGER) is a global partnershipbetween international and national agricultural research institutions. INGER focuses onworldwide exchange, evaluation and utilization of improved varieties and elite breedinglines of rice. China has actively participated in the activities of INGER since 1980.During the pasted years, 26500 INGER entries with diversity genetic background have beenintroduced and evaluated by Chinese scientists. Among of them, 37 commercial varietiesdirectly from elite INGER entries and 27 rice hybrids using INGER lines as their restorerlines/donors have been released to farmers in China. About 1900 INGER entries wereindirectly utilized as cross parents or pest resistant donors in various national andprovincial rice breeding programs. Based on the incomplete statistics, there were 14.5million cumulated hectares planting these varieties and hybrids, from which 5.44 MT ofincreased rough rice has been received by farmers. INGER accelerates the transfer ofadapted varieties and hybrids to farmers, and increases the diversity of rice germplasmin cultivation. Therefore, INGER cooperation has made great benefit both in economy andsociety in China.

Performances and Germplasm Evaluation of Quantitative Resistance to Soybean Mosaic Virus in Soybeans

A sample composed of 96 soybean accessions was evaluated for their diseased rate (I),diseased rank (S), latent period (LP) and rate of disease development (R) in order tostudy the quantitative resistance to soybean mosaic virus (SMV) in soybeans. The resultsshowed that the performances of the above four resistance components were significantlydifferent among accessions and that some of the accessions, such as Zhongzihuangdou,Peixian Tianedan, Youbian30 could be infected by four SMV strains, Sa, SC8, N1 and N3,but their I, S, and R were lower and LP longer than most other accessions. These resultsdemonstrated the existence of quantitative resistance to SMV in soybeans. It was foundthat some soybean accessions, such as AGS19 and Lishui Zhongzihuangdou, previouslyidentified as resistant to SMV infection, performed some infection but resistant toexpansion in the present study. In addition, the resistance in Pixian Chadou and HuaiyinQiuheidou might be either qualitative or quantitative. Furthermore, the present studyalso indicated that the resistance spectrum and durability of accessions with quantitativeresistance might be wider and longer than those with qualitative resistance.

Characterization of chickpea germplasm conserved in the Indian National Genebank and development of a core set using qualitative and quantitative trait data

Chickpea is the third most important pulse crop as a source of dietary protein. Ever-increasing demand in Asian countries calls for breeding superior desi-type varieties, in turn necessitating the availability of characterized germplasm to breeders. The Indian National Genebank,located at the National Bureau of Plant Genetic Resources, New Delhi, conserves 14,651 accessions of chickpea. The entire set was characterized in a single large-scale experiment.High variation was observed for eight quantitative and 12 qualitative agro-morphological traits. Allelic richness procedure was employed to assemble a core set comprising 1103 accessions, 70.0% of which were of Indian origin. Comparable values of total variation explained by the first three principal components in the entire collection(51.1%) and the core(52.4%)together with conservation of nine pairwise r values among quantitative traits in the core collection and a coincidence rate around 99.7% indicated that the chickpea core was indeed an excellent representation of the entire chickpea collection in the National Genebank. The chickpea core exhibited greater diversity than the entire collection in agro-morphological traits, as assessed by higher variance and Shannon–Weaver diversity indices, indicating that the chickpea core maximized the phenotypic diversity available in the Indian chickpea germplasm. The chickpea core, comprising mainly indigenous desi genotypes, is expected to be an excellent resource for chickpea breeders. Information on the chickpea core can be accessed at http://www.nbpgr.ernet.in/pgrportal.

Screening for Rice Germplasms with Specially-Elongated Mesocotyl

The lengths of mesocotyl in the seedlings of 84 lowland rice varieties and 12 upland rice varieties were measured following the treatments of daylight and darkness during germination. The elongation of mesocotyl in the varieties tested was inhibited under daylight condition, and the mesocotyl of all the varieties elongated variably under darkness condition. The elongated lengths of the mesocotyl in upland rice, ranging from 0.36 cm to 1,61 cm with an average of 0.81 cm, was obviously longer than those in lowland rice, ranging from 0.12 cm to 1.56 cm with an average of 0.42 cm. Among 14 rice varieties with over 1 cm of mesocotyl length, five belonged to upland rice, and nine to lowland rice. The possible utilization of the elongated-mesocotyl rice germplasm in varietal imorovement, direct-seeded plantina and seed ouritv testina were discussed.